Assembly and comparative analysis of the complete mitochondrial genome of Ilex metabaptista (Aquifoliaceae), a Chinese endemic species with a narrow distribution.

BACKGROUND: Ilex metabaptista is a woody tree species with strong waterlogging tolerance and is also admired as a landscape plant with high development prospects and scientific research value. Unfortunately, populations of this species have declined due to habitat loss. Thus, it is a great challenge for us to efficiently protect I. metabaptista resources from extinction. Molecular biology research can provide the scientific basis for the conservation of species. However, the study of I. metabaptista genetics is still in its infancy. To date, no mitochondrial genome (mitogenome) in the genus Ilex has been analysed in detail. RESULTS: The mitogenome of I. metabaptista was assembled based on the reads from Illumina and Nanopore sequencing platforms; it was a typical circular DNA molecule of 529,560 bp with a GC content of 45.61% and contained 67 genes, including 42 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 286 dispersed repeats, 140 simple repeats, 18 tandem repeats, and 543 RNA editing sites. Analysis of codon usage showed that codons ending in A/T were preferred. Gene migration was observed to occur between the mitogenome and chloroplast genome via the detection of homologous fragments. In addition, Ka/Ks analysis revealed that most of the protein-coding genes in the mitogenome had undergone negative selection, and only the ccmB gene had undergone potential positive selection in most asterids. Nucleotide polymorphism analysis revealed the variation in each gene, with atp9 being the most notable. Furthermore, comparative analysis showed that the GC contents were conserved, but the sizes and structure of mitogenomes varied greatly among asterids. Phylogenetic analysis based on the mitogenomes reflected the exact evolutionary and taxonomic status of I. metabaptista. CONCLUSION: In this study, we sequenced and annotated the mitogenome of I. metabaptista and compared it with the mitogenomes of other asterids, which provided essential background information for further understanding of the genetics of this plant and helped lay the foundation for future studies on molecular breeding of I. metabaptista.

A first insight into the genomic background of Ilex pubescens (Aquifoliaceae) by flow cytometry and genome survey sequencing.

BACKGROUND: Ilex pubescens is an important traditional Chinese medicinal plant with many naturally occurring compounds and multiple pharmacological effects. However, the lack of reference genomic information has led to tardiness in molecular biology research and breeding programs of this plant. RESULTS: To obtain knowledge on the genomic information of I. pubescens, a genome survey was performed for the first time by next generation sequencing (NGS) together with genome size estimation using flow cytometry. The whole genome survey of I. pubescens generated 46.472 Gb of sequence data with approximately 82.2 × coverage. K-mer analysis indicated that I. pubescens has a small genome of approximately 553 Mb with 1.93% heterozygosity rate and 39.1% repeat rate. Meanwhile, the genome size was estimated to be 722 Mb using flow cytometry, which was possibly more precise for assessment of genome size than k-mer analysis. A total of 45.842 Gb clean reads were assembled into 808,938 scaffolds with a relatively short N50 of 760 bp. The average guanine and cytosine (GC) content was 37.52%. In total, 197,429 microsatellite motifs were detected with a frequency of 2.8 kb, among which mononucleotide motifs were the most abundant (up to 62.47% of the total microsatellite motifs), followed by dinucleotide and trinucleotide motifs. CONCLUSION: In summary, the genome of I. pubescens is small but complex with a high level of heterozygosity. Even though not successfully applied for estimation of genome size due to its complex genome, the survey sequences will help to design whole genome sequencing strategies and provide genetic information support for resource protection, genetic diversity analysis, genetic improvement and artificial breeding of I. pubescens.

Complete chloroplast genome of Ilex dabieshanensis: Genome structure, comparative analyses with three traditional Ilex tea species, and its phylogenetic relationships within the family Aquifoliaceae.

Ilex dabieshanensis K. Yao & M. B. Deng is not only a highly valued tree species for landscaping, it is also a good material for making kuding tea due to its anti-inflammatory and lipid-lowering medicinal properties. Utilizing next-generation and long-read sequencing technologies, we assembled the whole chloroplast genome of I. dabieshanensis. The genome was 157,218 bp in length, exhibiting a typical quadripartite structure with a large single copy (LSC: 86,607 bp), a small single copy (SSC: 18,427 bp) and a pair of inverted repeat regions (IRA and IRB: each of 26,092 bp). A total of 121 predicted genes were encoded, including 113 distinctive (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions. Overall, 132 SSRs and 43 long repeats were detected and could be used as potential molecular markers. Comparative analyses of four traditional Ilex tea species (I. dabieshanensis, I. paraguariensis, I. latifolia and I. cornuta) revealed seven divergent regions: matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL. These variations might be applicable for distinguishing different species within the genus Ilex. Phylogenetic reconstruction strongly suggested that I. dabieshanensis formed a sister clade to I. cornuta and also showed a close relationship to I. latifolia. The generated chloroplast genome information in our study is significant for Ilex tea germplasm identification, phylogeny and genetic improvement.

Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships.

BACKGROUND: Ilex (Aquifoliaceae) are of great horticultural importance throughout the world for their foliage and decorative berries, yet a dearth of genetic information has hampered our understanding of phylogenetic relationships and evolutionary history. Here, we compare chloroplast genomes from across Ilex and estimate phylogenetic relationships. RESULTS: We sequenced the chloroplast genomes of seven Ilex species and compared them with 34 previously published Ilex plastomes. The length of the seven newly sequenced Ilex chloroplast genomes ranged from 157,182 bp to 158,009 bp, and contained a total of 118 genes, including 83 protein-coding, 31 rRNA, and four tRNA genes. GC content ranged from 37.6 to 37.69%. Comparative analysis showed shared genomic structures and gene rearrangements. Expansion and contraction of the inverted repeat regions at the LSC/IRa and IRa/SSC junctions were observed in 22 and 26 taxa, respectively; in contrast, the IRb boundary was largely invariant. A total of 2146 simple sequence repeats and 2843 large repeats were detected in the 41 Ilex plastomes. Additionally, six genes (psaC, rbcL, trnQ, trnR, trnT, and ycf1) and two intergenic spacer regions (ndhC-trnV and petN-psbM) were identified as hypervariable, and thus potentially useful for future phylogenetic studies and DNA barcoding. We recovered consistent phylogenetic relationships regardless of inference methodology or choice of loci. We recovered five distinct, major clades, which were inconsistent with traditional taxonomic systems. CONCLUSION: Our findings challenge traditional circumscriptions of the genus Ilex and provide new insights into the evolutionary history of this important clade. Furthermore, we detail hypervariable and repetitive regions that will be useful for future phylogenetic and population genetic studies.

Intestinal absorption mechanism of rotundic acid: Involvement of P-gp and OATP2B1.

ETHNOPHARMACOLOGICAL RELEVANCE: Ilicis Rotundae Cortex (IRC), the dried barks of Ilex rotunda Thunb. (Aquifoliaceae), has been used for the prevention or treatment of colds, tonsillitis, dysentery, and gastrointestinal diseases in folk medicine due to its antibacterial and anti-inflammatory effects. However, there is no report about the intestinal absorption of major compounds that support traditional usage. AIM OF STUDY: Considering the potential of rotundic acid (RA) - major biologically active pentacyclic triterpenes found in the IRC, this study was purposed to uncover the oral absorption mechanism of RA using in situ single-pass intestinal perfusion (SPIP) model, in vitro cell models (Caco-2, MDCKII-WT, MDCKII-MDR1, MDCKII-BCRP, and HEK293-OATP2B1 cells) and in vivo pharmacokinetics studies in rats. MATERIALS AND METHODS: The molecular properties (solubility, lipophilicity, and chemical stability) and the effects of principal parameters (time, compound concentrations, pH, paracellular pathway, and the different intestinal segments) were analyzed by liquid chromatography-tandem mass spectrometry. The susceptibility of RA to various inhibitors, such as P-gp inhibitor verapamil, BCRP inhibitor Ko143, OATP 2B1 inhibitor rifampicin, and absorption enhancer EGTA were assessed. RESULTS: RA was a compound with low water solubility (12.89 µg/mL) and strong lipophilicity (LogP = 4.1). RA was considered stable in all media during the SPIP and transport studies. The SPIP and cell experiments showed RA was moderate absorbed in the intestines and exhibited time, concentration, pH, and segment-dependent permeability. In addition, results from the cell model, in situ SPIP model as well as the in vivo pharmacokinetics studies consistently showed that verapamil, rifampicin, and EGTA might have significant effect on the intestinal absorption of RA. CONCLUSION: The mechanisms of intestinal absorption of RA might involve multiple transport pathways, including passive diffusion, the participation of efflux (i.e., P-gp) and influx (i.e., OATP2B1) transporters, and paracellular pathways.

LC-MS Metabolomics and Chemotaxonomy of Caffeine-Containing Holly ( Ilex) Species and Related Taxa in the Aquifoliaceae.

Ilex species have been consumed traditionally as medicinal teas worldwide. Though the presence of caffeine has been reported in several species, little is known about secondary-metabolite diversity within and among these taxa. Leaf samples of Ilex guayusa, Ilex paraguariensis, and Ilex vomitoria were analyzed by liquid chromatography-mass spectrometry and comparative metabolite profiling with Ilex cassine and other Ilex species to identify chemotaxonomic markers, delimit species, and provide an assessment of chemodiversity. Purine alkaloids were detected and quantified in I. guayusa, I. paraguariensis, and I. vomitoria. Reports of caffeine for I. cassine were not corroborated, suggesting that I. vomitoria was the traditional source of the Native North American tea yaupon. The tetramethyluric acid, theacrine, was detected for the first time in the genus Ilex as a low-level chemotaxonomic marker in I. vomitoria samples. Chemotaxonomy and metabolomics support a close relationship for caffeine-containing Ilex species.

Improved Soluble Expression and Catalytic Activity of a Thermostable Esterase Using a High-Throughput Screening System Based on a Split-GFP Assembly.

The thermostable esterase Aaeo1 displays a low expression level and forms a great amount of inclusion bodies in E. coli. Herein, a split-GFP system was established in which the fluorescence intensity exhibited a good linear correlation with the soluble protein expression level and the esterase activity. In the primary high-throughput screening, the mutant library was screened by flow cytometry via detection of a split-GFP reporter. Then, through a secondary screening against esterase activity, two mutants with improved soluble expression and catalytic activity were obtained. The soluble expression of the mutant enzymes in E. coli was improved by 2-fold. The kcat/ Km values of the mutant enzymes were 2-fold higher than that of the parent. We explored the relationship between the amino acid mutations in the two mutants and the enzyme activity. The enzyme activity of mutant I51V-E170D was 4.5 times higher than that of the parent.

Multiple zinc ions maintain the open conformation of the catalytic site in the DNA mismatch repair endonuclease MutL from Aquifex aeolicus.

The DNA mismatch repair endonuclease MutL consists of N-terminal ATPase and C-terminal endonuclease domains. The endonuclease domain binds zinc ion, although the ion seems not to function as a catalytic metal ion. Here, we solved the crystal structures of the Aquifex aeolicus MutL (aqMutL) endonuclease domain complexed with a single and three zinc ions. Differences between the two structures show that binding of multiple zinc ions induces a closed-to-open conformational change at the catalytic site. It is also revealed that the three-zinc-bound form of the endonuclease domain exhibits higher endonuclease activity than the single-zinc-bound form. These results indicate that multiple zinc ions are required for the proper folding of the endonuclease domain, which would facilitate the endonuclease activity of aqMutL.

Rational Design of Domain-Swapping-Based c-Type Cytochrome Heterodimers by Using Chimeric Proteins.

The design of protein oligomers with multiple active sites has been gaining interest, owing to their potential use for biomaterials, which has encouraged researchers to develop a new design method. Three-dimensional domain swapping is the unique phenomenon in which protein molecules exchange the same structural region between each other. Herein, to construct oligomeric heme proteins with different active sites by utilizing domain swapping, two c-type cytochrome-based chimeric proteins have been constructed and the domains swapped. According to X-ray crystallographic analysis, the two chimeric proteins formed a domain-swapped dimer with two His/Met coordinated hemes. By mutating the heme coordination structure of one of the two chimeric proteins, a domainswapped heterodimer with His/Met and His/H2 O coordinated hemes was formed. Binding of an oxygen molecule to the His/H2 O site of the heterodimer was confirmed by resonance Raman spectroscopy, in which the Fe-O2 stretching band was observed at 580 cm-1 for the reduced/oxygenated heterodimer (at 554 cm-1 under an 18 O2 atmosphere). These results show that domain swapping is a useful method to design multiheme proteins.

Sexual and vegetative propagation of the medicinal Mexican species Phyllonoma laticuspis (Phyllonomaceae) / Propagación sexual y vegetativa de la especie medicinal mexicana Phyllonoma laticuspis (Phyllonomaceae)

Abstract:Phyllonoma laticuspis leaves are used in Carrizal de Bravo, Guerrero, Mexico, to heal skin lesions such as injuries and smallpox sequelae and to treat diabetes mellitus type 2, and organic extracts of these leaves have been reported to exert antibacterial effects. High demand of P. laticuspis as a medicinal plant has decreased its natural populations, and propagation of the species has not yet been reported. Therefore, the purpose of this study was to assess the vegetative propagation of the species through cutting and air layering, as well as its sexual propagation in a preserved population. For this, concentrations of 1 000, 4 000 and 6 000 ppm of a commercial root enhancer, with indole butyric acid (IBA), and a control treatment without IBA, were applied to the cuttings and air layers. Germination was evaluated under light and dark conditions using lots of freshly collected seeds and lots of seeds that had been stored for three months at 4 °C or 24 ± 2 °C. All experiments were performed in a completely randomized design. The cuttings did not develop roots in any concentration, whereas 100 % of the air layers rooted, displaying vigorous roots in the presence of 4 000 ppm IBA, after four month of treatment application. Regarding germination, more than 60 % of the freshly collected seeds germinated, whereas less than 20 % of the seeds stored at 4 °C, and close to 50 % of the seeds stored at 24 ± 2 °C germinated under light and dark conditions. No significant differences were observed between light and dark conditions, so they were categorized as indifferent photoblastic seeds. The observed moisture content of 13.5 % and germination behaviour as the response to cold storage, suggest that the resultant seed quality was intermediate. P. laticuspis propagation for short-term foliage production can be carried out in air layers, in populations with a high density of adult plants as a source of plant material and for the restoration of disturbed areas, in the same locality. On the other hand, large-scale seedling production, medium-term foliage production and preservation of species variability can be achieved using seeds. Rev. Biol. Trop. 65 (1): 9-19. Epub 2017 March 01.

ResumenLas hojas de Phyllonoma laticuspis se utilizan en Carrizal de Bravo, Gro. México, para curar lesiones de la piel como heridas, secuelas de viruela y afecciones de la diabetes mellitus tipo 2. Los extractos orgánicos de hojas, mostraron efectos antibacterianos. La gran demanda de P. laticuspis como planta medicinal, ha disminuido sus poblaciones naturales, y no existen reportes de la propagación de la especie. Por lo tanto, el propósito del presente trabajo fue evaluar la propagación vegetativa de la especie a través de estacas y acodos, y su propagación sexual en una población conservada. En la propagación por estacas y acodos se aplicaron concentraciones de 1 000, 4 000 y 6 000 ppm de un enraizador comercial con ácido indolbutírico (AIB), y un tratamiento control sin AIB. La germinación se evaluó en luz y oscuridad mediante el uso de lotes de semillas recién recolectadas y lotes de semillas almacenadas por tres meses a 4 °C y a 24 ± 2 ºC. Todos los experimentos se realizaron en un diseño completamente al azar. Las estacas no desarrollaron raíces en ninguna de las concentraciones, mientras que el 100 % de los acodos enraizaron, produciendo raíces vigorosas con la concentración de 4 000 ppm de AIB, a los cuatro meses de la aplicación. Con respecto a la germinación bajo condiciones de luz y oscuridad, las semillas recién recolectadas germinaron más del 60 %, mientras que las semillas almacenadas a 4 ºC menos del 20 % y las almacenadas a 24 ± 2 ºC cerca del 50 %. No hubieron diferencias significativas entre la germinación en luz y oscuridad, por lo que se consideraron como semillas fotoblásticas indiferentes. El contenido de humedad de 13.5 % y el comportamiento de la germinación en respuesta al almacenamiento en frío, sugieren la cualidad de semillas de tipo intermedias. La propagación de P. laticuspis para la producción de follaje a corto tiempo, puede hacerse por acodos en poblaciones con alta densidad de plantas adultas como fuente de material vegetal y para la restauración de áreas alteradas en la misma localidad. Mientras que la producción de follaje a mediano plazo y la conservación de la variabilidad de la especie, se puede lograr con la obtención masiva de plántulas a través de semillas.

Ilexgenin A, a novel pentacyclic triterpenoid extracted from Aquifoliaceae shows reduction of LPS-induced peritonitis in mice.

Ilexgenin A (IA) is a novel pentacyclic triterpenoid, which extracted from leaves of Ilex hainanensis Merr. In the present study, we aim to explore anti-inflammatory activity of IA on LPS-induced peritonitis and its underlying molecular mechanism. The results determined that IA was capable of suppressing peritonitis in mice induced by intraperitoneal (i.p.) injection of lipopolysaccaride (LPS). Furthermore, the results showed that IA dramatically inhibited levels of inflammatory cells infiltration in peritoneal cavity and serum in LPS-induced mice peritonitis model. Besides, IA could dramatically inhibit levels of inflammatory cytokines (IL-1ß, IL-6 and TNF-α) in peritoneal cavity in LPS-induced mice peritonitis model. In vitro study, the results showed that IA inhibited production of IL-1ß, IL-6 and TNF-α at transcriptional and translational levels in RAW 264.7 cells induced by LPS. Furthermore, IA could suppress the LPS-induced activation of Akt and downstream degradation and phosphorylation of kappa B-α (IκB-α). Moreover, IA could significantly inhibit ERK 1/2 phosphorylation in RAW 264.7 cells induced by LPS. These results were concurrent with molecular docking which revealed ERK1/2 inhibition. These results demonstrated that IA might as an anti-inflammatory agent candidate for inflammatory disease therapy.

Chemoenzyamtic synthesis and self-assembling gelation behavior of amylose-grafted poly(γ-glutamic acid).

In this study, we investigated chmemoenzymatic synthesis of amylose-grafted poly(γ-glutamic acid) (PGA) as a new artificial saccharide-peptide conjugate composed of two biological macromolecules. Maltooligosaccharide as a primer of enzymatic polymerization by phosphorylase catalysis was first introduced on the PGA main chain by the condensation reaction using the condensing agent in NaOH aq. Thermostable phosphorylase-catalyzed enzymatic polymerization of α-d-glucose 1-phosphate (G-1-P) as a monomer was then performed from the primer chain ends of the product to obtain amylose-grafted PGAs, which formed hydrogels in reaction media depending on the G-1-P/primer feed ratios. The powder X-ray diffraction patterns of lyophilized samples (cryogels) from the hydrogels suggested that the amylose graft chains formed double helixes, which acted as cross-inking points for self-assembling hydrogelation. The scanning electron microscopic images of the cryogels showed regularly controlled porous morphologies. Moreover, pore sizes of the cryogels increased with increasing the G-1-P/primer feed ratios, whereas the degrees of substitution of primer on the PGA main chain did not obviously affect pore sizes.

Sexual and vegetative propagation of the medicinal Mexican species Phyllonoma laticuspis (Phyllonomaceae).

Phyllonoma laticuspis leaves are used in Carrizal de Bravo, Guerrero, Mexico, to heal skin lesions such as injuries and smallpox sequelae and to treat diabetes mellitus type 2, and organic extracts of these leaves have been reported to exert antibacterial effects. High demand of P. laticuspis as a medicinal plant has decreased its natural populations, and propagation of the species has not yet been reported. Therefore, the purpose of this study was to assess the vegetative propagation of the species through cutting and air layering, as well as its sexual propagation in a preserved population. For this, concentrations of 1 000, 4 000 and 6 000 ppm of a commercial root enhancer, with indole butyric acid (IBA), and a control treatment without IBA, were applied to the cuttings and air layers. Germination was evaluated under light and dark conditions using lots of freshly collected seeds and lots of seeds that had been stored for three months at 4 °C or 24 ± 2 °C. All experiments were performed in a completely randomized design. The cuttings did not develop roots in any concentration, whereas 100 % of the air layers rooted, displaying vigorous roots in the presence of 4 000 ppm IBA, after four month of treatment application. Regarding germination, more than 60 % of the freshly collected seeds germinated, whereas less than 20 % of the seeds stored at 4 °C, and close to 50 % of the seeds stored at 24 ± 2 °C germinated under light and dark conditions. No significant differences were observed between light and dark conditions, so they were categorized as indifferent photoblastic seeds. The observed moisture content of 13.5 % and germination behaviour as the response to cold storage, suggest that the resultant seed quality was intermediate. P. laticuspis propagation for short-term foliage production can be carried out in air layers, in populations with a high density of adult plants as a source of plant material and for the restoration of disturbed areas, in the same locality. On the other hand, large-scale seedling production, medium-term foliage production and preservation of species variability can be achieved using seeds.

Embryology of Cardiopteris (Cardiopteridaceae, Aquifoliales), with emphasis on unusual ovule and seed development.

Cardiopteris (Cardiopteridaceae), a twining herb of two or three species distributed from Southeast Asia to Northern Australia, requires an embryological study for better understanding of its reproductive features. The present study of C. quinqueloba showed that the ovule and seed development involves a number of unusual structures, most of which are unknown elsewhere in angiosperms. The ovule pendant from the apical placenta is straight (not orthotropous), ategmic, and tenuinucellate, developing a monosporic seven-celled/eight-nucleate female gametophyte with an egg apparatus on the funicular side. Fertilization occurs by a pollen tube entering from the funicular side, resulting in a zygote on the funicular side. The endosperm is formed by the cell on the funicular side in the two endosperm cell stage. While retaining a (pro)embryo/endosperm as it is, the raphe (differentiating late in pre-fertilization stages) elongates toward the antiraphal side during post-fertilization stages, resulting in an anatropous seed. The two-cell-layered nucellar epidermis (belatedly forming by periclinal divisions), along with the raphe, envelops the embryo/endosperm entirely as the seed coat. The possibility was discussed that the arrested integument development triggers a series of the subsequent unusual structures of ovule and seed development. The fertilization mode in Cardiopteris underpins the hypothesis that the Polygonum‒type female gametophyte comprises two four-celled archegonia.

Domain swapping oligomerization of thermostable c-type cytochrome in E. coli cells.

Knowledge on domain swapping in vitro is increasing, but domain swapping may not occur regularly in vivo, and its information in cells is limited. Herein, we show that domain-swapped oligomers of a thermostable c-type cytochrome, Hydrogenobacter thermophilus cyt c552, are formed in E. coli which expresses cyt c552. The region containing the N-terminal α-helix and heme was domain-swapped between protomers in the dimer formed in E. coli. The amount of cyt c552 oligomers increased in E. coli as the cyt c552 concentration was increased, whereas that of high-order oligomers decreased in the order of decrease in protein stability, indicating that domain swapping decreases in cells when the protein stability decreases. Apo cyt c552 was detected in the cyt c552 oligomer formed in E. coli, but not in that of the A5F/M11V/Y32F/Y41E/I76V mutant. The cyt c552 oligomer containing its apo protein may form at the periplasm, since the apo protein detected by mass measurements did not contain the signal peptide. These results show that domain-swapped cyt c552 oligomers were formed in E. coli, owing to the stability of the transient oligomer containing the apo protein before heme attachment. This is an indication that exceedingly stable proteins may have disadvantages forming domain-swapped oligomers in cells.

Hydrogen bioelectrooxidation on gold nanoparticle-based electrodes modified by Aquifex aeolicus hydrogenase: Application to hydrogen/oxygen enzymatic biofuel cells.

For the first time, gold nanoparticle-based electrodes have been used as platforms for efficient immobilization of the [NiFe] hydrogenase from the hyperthermophilic bacterium Aquifex aeolicus. AuNPs were characterized by electronic microscopy, dynamic light scattering and UV-Vis spectroscopy. Two sizes around 20.0±5.3 nm and 37.2±4.3 nm nm were synthesized. After thiol-based functionalization, the AuNPs were proved to allow direct H2 oxidation over a large range of temperatures. A high current density up to 1.85±0.15 mA·cm(-2) was reached at the smallest AuNPs, which is 170 times higher than the one recorded at the bare gold electrode. The catalytic current was especially studied as a function of the AuNP size and amount, and procedure for deposition. A synergetic effect between the AuNP porous deposit and the increase surface area was shown. Compared to previously used nanomaterials such as carbon nanofibers, the covalent grafting of the enzyme on the thiol-modified gold nanoparticles was shown to enhance the stability of the hydrogenase. This bioanode was finally coupled to a biocathode where BOD from Myrothecium verrucaria was immobilized on AuNP-based film. The performance of the so-mounted H2/O2 biofuel cell was evaluated, and a power density of 0.25 mW·cm(-2) was recorded.

Spectroscopic and redox studies of valence-delocalized [Fe2S2](+) centers in thioredoxin-like ferredoxins.

Reduced forms of the C56S and C60S variants of the thioredoxin-like Clostridium pasteurianum [Fe2S2] ferredoxin (CpFd) provide the only known examples of valence-delocalized [Fe2S2](+) clusters, which constitute a fundamental building block of all higher nuclearity Fe-S clusters. In this work, we have revisited earlier work on the CpFd variants and carried out redox and spectroscopic studies on the [Fe2S2](2+,+) centers in wild-type and equivalent variants of the highly homologous and structurally characterized Aquifex aeolicus ferredoxin 4 (AaeFd4) using EPR, UV-visible-NIR absorption, CD and variable-temperature MCD, and protein-film electrochemistry. The results indicate that the [Fe2S2](+) centers in the equivalent AaeFd4 and CpFd variants reversibly interconvert between similar valence-localized S = 1/2 and valence-delocalized S = 9/2 forms as a function of pH, with pKa values in the range 8.3-9.0, because of protonation of the coordinated serinate residue. However, freezing high-pH samples results in partial or full conversion from valence-delocalized S = 9/2 to valence-localized S = 1/2 [Fe2S2](+) clusters. MCD saturation magnetization data for valence-delocalized S = 9/2 [Fe2S2](+) centers facilitated determination of transition polarizations and thereby assignments of low-energy MCD bands associated with the Fe-Fe interaction. The assignments provide experimental assessment of the double exchange parameter, B, for valence-delocalized [Fe2S2](+) centers and demonstrate that variable-temperature MCD spectroscopy provides a means of detecting and investigating the properties of valence-delocalized S = 9/2 [Fe2S2](+) fragments in higher nuclearity Fe-S clusters. The origin of valence delocalization in thioredoxin-like ferredoxin Cys-to-Ser variants and Fe-S clusters in general is discussed in light of these results.

Synthesis of chitin and chitosan stereoisomers by thermostable α-glucan phosphorylase-catalyzed enzymatic polymerization of α-D-glucosamine 1-phosphate.

The relationship between two aminopolysaccharide stereoisomers, namely α-(1→4)- and ß-(1→4)-linked (N-acetyl)-D-glucosamine polymers, is of significant interest within the field of polysaccharide science, as they correspond to amino analogs of the representative abundant natural polysaccharides, viz. amylose and cellulose. While the latter glucosamine polymer is the basis of well-known natural polysaccharides, chitin and chitosan (linear polysaccharides composed of ß-(1→4)-linked N-acetyl-D-glucosamine and D-glucosamine), to the best of our knowledge, the former (α-(1→4)-linked) has not been observed in nature. For the purpose of these studies, the synthesis of such non-natural aminopolysaccharides was performed by the thermostable α-glucan phosphorylase (from Aquifex aeolicus VF5)-catalyzed enzymatic polymerization of α-D-glucosamine 1-phosphate (GlcN-1-P), via successive α-glucosaminylations, in ammonia buffer containing Mg(2+) ions, resulting in the production of the α-(1→4)-linked D-glucosamine polymers, corresponding to the structure of the chitosan stereoisomer. Subsequent N-acetylation of the products gave the aminopolysaccharides, corresponding to the chitin stereoisomer.

Construction of Matryoshka-type structures from supercharged protein nanocages.

Designing nanoscaled hierarchical structures with increasing levels of complexity is challenging. Here we show that electrostatic interactions between two complementarily supercharged protein nanocages can be effectively utilized to create nested Matryoshka-type structures. Cage-within-cage complexes containing spatially ordered iron oxide nanoparticles spontaneously self-assemble upon mixing positively supercharged ferritin compartments with AaLS-13, a larger shell-forming protein with a negatively supercharged lumen. Exploiting engineered Coulombic interactions and protein dynamics in this way opens up new avenues for creating hierarchically organized supramolecular assemblies for application as delivery vehicles, reaction chambers, and artificial organelles.

Multiscale simulations give insight into the hydrogen in and out pathways of [NiFe]-hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans.

[NiFe]-hydrogenases catalyze the cleavage of molecular hydrogen into protons and electrons and represent promising tools for H2-based technologies such as biofuel cells. However, many aspects of these enzymes remain to be understood, in particular how the catalytic center can be protected from irreversible inactivation by O2. In this work, we combined homology modeling, all-atom molecular dynamics, and coarse-grain Brownian dynamics simulations to investigate and compare the dynamic and mechanical properties of two [NiFe]-hydrogenases: the soluble O2-sensitive enzyme from Desulfovibrio fructosovorans, and the O2-tolerant membrane-bound hydrogenase from Aquifex aeolicus. We investigated the diffusion pathways of H2 from the enzyme surface to the central [NiFe] active site, and the possible proton pathways that are used to evacuate hydrogen after the oxidation reaction. Our results highlight common features of the two enzymes, such as a Val/Leu/Arg triad of key residues that controls ligand migration and substrate access in the vicinity of the active site, or the key role played by a Glu residue for proton transfer after hydrogen oxidation. We show specificities of each hydrogenase regarding the enzymes internal tunnel network or the proton transport pathways.