Multiple buds are an alternative target to genetic manipulation of kenaf (Hibiscus cannabinus L.)

Kenaf (Hibiscus cannabinus L.) is an annual fiber crop cultivated as an important source of cellulose and lignin. In the recent years, fibers have increased their economic importance as organic component in bio-composite materials. However, industry requires rheological improvements of these fibers. Genetic manipulation has been considered a feasible approach for fiber improvement; however, kenaf is considered a crop species difficult to manipulate. Here we propose meristematic cells from mature embryos as target for genetic modification driven by Agrobacterium tumefaciens. In vitro meristems proliferation and multiple shoots regeneration were evaluated by sowing kenaf mature seeds on medium containing three different concentration of thidiazuron, a substituted urea compound. The highest number of regenerated shoots was obtained from mature seeds germinated in presence of 10 μM thidiazuron after 14 days of culture. Interactions between two A. tumefaciens strains and two kenaf varieties were assessed. Transgene stable integration and its inheritance in T₁ generation were also verified, demonstrating that kenaf meristematic cells are an useful target for genetic manipulation by agroinfection.     

Kenaf (Hibiscus cannabinus L.) based substrates for the production of compact plants

Growth media based on whole-stem kenaf (Hibiscus cannabinus L.) and sand have been used to produce compact lettuce (Lactuca sativa L.) and pepper (Capsicum annuum L.) plants. Seeds were sown directly in kenaf-containing substrates and growth was recorded for up to 100 days after sowing. The presence of whole-stem kenaf (core and bark), even at a ratio of 10:90 (kenaf:sand), inhibited plant growth expressed as plant height, leaf number, and plant fresh and dry weight. When plants were subsequently transplanted to a kenaf-free substrate, growth continued at a similar rate to that of the control (sown and grown in peat and sand). The inhibitory effect of kenaf is located both in the core and bark, but is decreased by soaking the kenaf in NH₄NO₃ prior to use. A possible role for whole-stem kenaf (core and bark) in the production of compact plants is proposed.     

Sensitivity of Neurospora crassa to a Marine-Derived Aspergillus tubingensis Anhydride Exhibiting Antifungal Activity That Is Mediated by the MAS1 Protein

The fungus Aspergillus tubingensis (strain OY907) was isolated from the Mediterranean marine sponge Ircinia variabilis. Extracellular extracts produced by this strain were found to inhibit the growth of several fungi. Among the secreted extract components, a novel anhydride metabolite, tubingenoic anhydride A (1) as well as the known 2-carboxymethyl-3-hexylmaleic acid anhydride, asperic acid, and campyrone A and C were purified and their structure elucidated. Compound 1 and 2-carboxymethyl-3-hexylmaleic acid anhydride inhibited Neurospora crassa growth (MIC = 330 and 207 μM, respectively) and affected hyphal morphology. We produced a N. crassa mutant exhibiting tolerance to 1 and found that a yet-uncharacterized gene, designated mas-1, whose product is a cytosolic protein, confers sensitivity to this compound. The ∆mas-1 strain showed increased tolerance to sublethal concentrations of the chitin synthase inhibitor polyoxin D, when compared to the wild type. In addition, the expression of chitin synthase genes was highly elevated in the ∆mas-1 strain, suggesting the gene product is involved in cell wall biosynthesis and the novel anhydride interferes with its function.     

Diversity and Biosynthetic Potential of Culturable Microbes Associated with Toxic Marine Animals

Tetrodotoxin (TTX) is a neurotoxin that has been reported from taxonomically diverse organisms across 14 different phyla. The biogenic origin of tetrodotoxin is still disputed, however, TTX biosynthesis by host-associated bacteria has been reported. An investigation into the culturable microbial populations from the TTX-associated blue-ringed octopus Hapalochlaena sp. and sea slug Pleurobranchaea maculata revealed a surprisingly high microbial diversity. Although TTX was not detected among the cultured isolates, PCR screening identifiedsome natural product biosynthesis genes putatively involved in its assembly. This study is the first to report on the microbial diversity of culturable communities from H. maculosa and P. maculata and common natural product biosynthesis genes from their microbiota. We also reassess the production of TTX reported from three bacterial strains isolated from the TTX-containing gastropod Nassarius semiplicatus.     

High value triterpenic compounds from the outer barks of several Eucalyptus species cultivated in Brazil and in Portugal

The chemical composition of the lipophilic extracts of the inner and outer bark fractions of Eucalyptus grandis and Eucalyptus urograndis (E. grandis × Eucalyptus urophylla) cultivated in Brazil and Eucalyptus maidenii, cultivated in Portugal was studied by gas chromatography-mass spectrometry. The extracts were shown to be mainly composed of triterpenic compounds (along with mono and sesquiterpenes in E. maidenii) followed smaller amounts of fatty acids, fatty alcohols, and aromatic compounds.Triterpenic acids (mainly ursolic, betulinic and oleanolic acids), are particularly abundant in outer barks representing 5.2 g/kg, 5.7 g/kg and 9.3 g/kg in E. urograndis, E. grandis and E. maidenii outer barks, respectively. Although these compounds were found in considerably smaller amounts than those previously reported for Eucalyptus globulus, the total amounts of bark generated every year in South American pulp mills using E. urograndis and E. grandis, as well as the growth potential of E. maidenii plantations, the bark residues from these species are obvious candidates for the extraction of valuable triterpenic compounds.     

Molecular and Chemical Analysis of the Lipopolysaccharide from Aeromonas hydrophila Strain AH-1 (Serotype O11)

A group of virulent Aeromonas hydrophila, A. sobria, and A. veronii biovar sobria strains isolated from humans and fish have been described; these strains classified to serotype O11 are serologically related by their lipopolysaccharide (LPS) O-antigen (O-polysaccharide), and the presence of an S-layer consisting of multiple copies of a crystalline surface array protein with a molecular weight of 52 kDa in the form of a crystalline surface array which lies peripheral to the cell wall. A. hydrophila strain AH-1 is one of them. We isolated the LPS from this strain and determined the structure of the O-polysaccharide, which was similar to that previously described for another strain of serotype O11. The genetics of the O11-antigen showed the genes (wb_O11 cluster) in two sections separated by genes involved in biosynthesis and assembly of the S-layer. The O11-antigen LPS is an example of an ABC-2-transporter-dependent pathway for O-antigen heteropolysaccharide (disaccharide) assembly. The genes involved in the biosynthesis of the LPS core (waa_O11 cluster) were also identified in three different chromosome regions being nearly identical to the ones described for A. hydrophila AH-3 (serotype O34). The genetic data and preliminary chemical analysis indicated that the LPS core for strain AH-1 is identical to the one for strain AH-3.     

Promoter Trapping in Microalgae Using the Antibiotic Paromomycin as Selective Agent

The lack of highly active endogenous promoters to drive the expression of transgenes is one of the main drawbacks to achieving efficient transformation of many microalgal species. Using the model chlorophyte Chlamydomonas reinhardtii and the paromomycin resistance APHVIII gene from Streptomyces rimosus as a marker, we have demonstrated that random insertion of the promoterless marker gene and subsequent isolation of the most robust transformants allows for the identification of novel strong promoter sequences in microalgae. Digestion of the genomic DNA with an enzyme that has a unique restriction site inside the marker gene and a high number of target sites in the genome of the microalga, followed by inverse PCR, allows for easy determination of the genomic region, which precedes the APHVIII marker gene. In most of the transformants analyzed, the marker gene is inserted in intragenic regions and its expression relies on its adequate insertion in frame with native genes. As an example, one of the new promoters identified was used to direct the expression of the APHVIII marker gene in C. reinhardtii, showing high transformation efficiencies.     

Improving the use of kenaf for kraft pulping by using mixtures of bast and core fibers

Kenaf (Hibiscus cannabinus L.) is a herbaceous annual plant amenable to use as a papermaking raw material. Kraft and soda pulping of kenaf have so far been done exclusively on the bark fraction (about 34–38% of the stem) or whole stem of the plant. Using kenaf bark exploits the higher quality of its bast fibers but reduces the typically high crop yields of this plant. In any case, core kraft pulp has acceptable properties some of which (e.g. tensile index, burst index) can even surpass those of bark pulp. Pulp made from both fractions has been found to exhibit better bonding properties than bark pulp. However, too high a proportion of core fibers can result in difficult drainage, a low tear strength or poor air permeability. These problems restrict the proportion of core that can be mixed with bast fibers, hinders separation of the two fractions and raises operational costs.The primary purpose of this study was to examine the influence of the core–bark ratio on the properties of mixed kenaf pulp. We used unrefined core pulp and refined bark pulp. Based on the results for kraft sacks, obtaining kenaf paper from both fractions has some advantages. Because Gurley air porosity changed dramatically with the proportion of core pulp used, it was used to determine the maximum amount of core fibers to be added to bast fibers. A proportion of up to 34% was found to have no adverse effect on air permeability. Such a proportion allowed paper strength to be preserved with an acceptable tear index (19.8 mN m²/g) and excellent tensile index (72 N m/g). Also, energy consumption was reduced if only the bark fraction was refined. The proposed strategy thus provides increased fiber yields of kenaf per hectare per year and valorizes the core fraction.     

Isolation and Analysis of the Cppsy Gene and Promoter from Chlorella protothecoides CS-41

Phytoene synthase (PSY) catalyzes the condensation of two molecules of geranylgeranyl pyrophosphate to form phytoene, the first colorless carotene in the carotenoid biosynthesis pathway. So it is regarded as the crucial enzyme for carotenoid production, and has unsurprisingly been involved in genetic engineering studies of carotenoid production. In this study, the psy gene from Chlorella protothecoides CS-41, designated Cppsy, was cloned using rapid amplification of cDNA ends. The full-length DNA was 2488 bp, and the corresponding cDNA was 1143 bp, which encoded 380 amino acids. Computational analysis suggested that this protein belongs to the Isoprenoid_Biosyn_C1 superfamily. It contained the consensus sequence, including three predicted substrate-Mg²⁺ binding sites. The Cppsy gene promoter was also cloned and characterized. Analysis revealed several candidate motifs for the promoter, which exhibited light- and methyl jasmonate (MeJA)-responsive characteristics, as well as some typical domains universally discovered in promoter sequences, such as the TATA-box and CAAT-box. Light- and MeJA treatment showed that the Cppsy expression level was significantly enhanced by light and MeJA. These results provide a basis for genetically modifying the carotenoid biosynthesis pathway in C. protothecoides.     

Metabolomic Profiling and Genomic Study of a Marine Sponge-Associated Streptomyces sp

Metabolomics and genomics are two complementary platforms for analyzing an organism as they provide information on the phenotype and genotype, respectively. These two techniques were applied in the dereplication and identification of bioactive compounds from a Streptomyces sp. (SM8) isolated from the sponge Haliclona simulans from Irish waters. Streptomyces strain SM8 extracts showed antibacterial and antifungal activity. NMR analysis of the active fractions proved that hydroxylated saturated fatty acids were the major components present in the antibacterial fractions. Antimycin compounds were initially putatively identified in the antifungal fractions using LC-Orbitrap. Their presence was later confirmed by comparison to a standard. Genomic analysis of Streptomyces sp. SM8 revealed the presence of multiple secondary metabolism gene clusters, including a gene cluster for the biosynthesis of the antifungal antimycin family of compounds. The antimycin gene cluster of Streptomyces sp. SM8 was inactivated by disruption of the antimycin biosynthesis gene antC. Extracts from this mutant strain showed loss of antimycin production and significantly less antifungal activity than the wild-type strain. Three butenolides, 4,10-dihydroxy-10-methyl-dodec-2-en-1,4-olide (1), 4,11-dihydroxy-10-methyl-dodec-2-en-1,4-olide (2), and 4-hydroxy-10-methyl-11-oxo-dodec-2-en-1,4-olide (3) that had previously been reported from marine Streptomyces species were also isolated from SM8. Comparison of the extracts of Streptomyces strain SM8 and its host sponge, H. simulans, using LC-Orbitrap revealed the presence of metabolites common to both extracts, providing direct evidence linking sponge metabolites to a specific microbial symbiont.     

Violacein-Producing Collimonas sp. from the Sea Surface Microlayer of Costal Waters in Tr?ndelag,Norway

A new strain belonging to the genus Collimonas was isolated from the sea surface microlayer off the coast of Trøndelag, Norway. The bacterium, designated Collimonas CT, produced an antibacterial compound active against Micrococcus luteus. Subsequent studies using LC-MS identified this antibacterial compound as violacein, known to be produced by several marine-derived bacteria. Fragments of the violacein biosynthesis genes vioA and vioB were amplified by PCR from the Collimonas CT genome and sequenced. Phylogenetic analysis of these sequences demonstrated close relatedness of the Collimonas CT violacein biosynthetic gene cluster to those in Janthinobacterium lividum and Duganella sp., suggesting relatively recent horizontal gene transfer. Considering diverse biological activities of violacein, Collimonas CT shall be further studied as a potential producer of this compound.     

Natural Product Chemistry of Gorgonian Corals of the Family Plexauridae Distributed in the Indo-Pacific Ocean

The structures, names, bioactivities and references of 105 natural products obtained from gorgonian corals belonging to the family Plexauridae with an Indo-Pacific distribution are described in this review. All compounds mentioned in this review were obtained from gorgonian corals belonging to the genera Astrogorgia, Bebryce, Echinomuricea, Euplexaura and Menella.     

Mild peroxyformic acid fractionation of Miscanthus × giganteus bark. Behaviour and structural characterization of lignin

Miscanthus × giganteus bark was subjected to mild fractionation with peroxyformic acid by a two stage process. A factorial experimental design was used to study and quantify the effect of the variables (formic acid concentration (80-90%), hydrogen peroxide concentration (0.2-0.4%), temperature of the first stage (60-80 °C), and treatment time of the second stage (60-120 min)) on the main parameters of fractionation: pulp yield, remaining lignin and total polysaccharides in pulp. The dependence of lignin precipitation rate on hydrogen peroxide concentration in liquor was also studied. Hydrogen peroxide concentrations inferior to 0.5% seems to be suitable to recover high percentages of lignin. The isolated lignin was analysed by 2D-HSQC, ¹³C- and ³¹P NMR spectroscopy, FTIR spectroscopy, size-exclusion chromatography and chemical analysis. The most important chemical modifications taken place in the lignin during the fractionation were identified: β-O-4′ cleavage and hydrolysis of LC-bond structures. The C9-formula was also determined: C₉H_6.81O_2.90(OCH₃)_0.68(COOH)_0.07(OH^Ph)_0.38(OH^Al)_0.33.     

Gene Sequence Based Clustering Assists in Dereplication of Pseudoalteromonas luteoviolacea Strains with Identical Inhibitory Activity and Antibiotic Production

Some microbial species are chemically homogenous, and the same secondary metabolites are found in all strains. In contrast, we previously found that five strains of P. luteoviolacea were closely related by 16S rRNA gene sequence but produced two different antibiotic profiles. The purpose of the present study was to determine whether such bioactivity differences could be linked to genotypes allowing methods from phylogenetic analysis to aid in selection of strains for biodiscovery. Thirteen P. luteoviolacea strains divided into three chemotypes based on production of known antibiotics and four antibacterial profiles based on inhibition assays against Vibrio anguillarum and Staphylococcus aureus. To determine whether chemotype and inhibition profile are reflected by phylogenetic clustering we sequenced 16S rRNA, gyrB and recA genes. Clustering based on 16S rRNA gene sequences alone showed little correlation to chemotypes and inhibition profiles, while clustering based on concatenated 16S rRNA, gyrB, and recA gene sequences resulted in three clusters, two of which uniformly consisted of strains of identical chemotype and inhibition profile. A major time sink in natural products discovery is the effort spent rediscovering known compounds, and this study indicates that phylogeny clustering of bioactive species has the potential to be a useful dereplication tool in biodiscovery efforts.     

Chemical characterization of barks from Picea abies and Pinus sylvestris after fractioning into different particle sizes

The composition of Norway spruce (Picea abies (L.) Karst.) and Scots pine (Pinus sylvestris L.) barks was studied after grinding and fractioning into different particles sizes.Both barks fractionated well and with similar fraction yield profile. The yield of fines was low and the major fractions were larger particles, i.e. 2.4% and 3.1% of particles under 0.425 mm and 66.0% and 50.3% of particles over 2 mm, respectively for spruce and pine bark.The chemical composition of spruce and pine barks, as a mass weighed average of all granulometric fractions was, respectively: ash 3.3 and 4.6%; total extractives 21.6 and 18.8% (hydrophilic extractives were dominant), lignin 27.9 and 33.7% and holocellulose 42.7 and 37.6%. Suberin accounted for 1.3% and 1.6% of spruce and pine bark, respectively. The non-cellulosic monosaccharides showed in both barks predominance of arabinose followed by xylose and mannose.Ash elemental composition showed that N represented about 35% of the total inorganics, Ca 35% and K 17%. Zn, Cu, Ni, Cr and Pb were present in both barks at levels under 1% of the total inorganics. Spruce bark had in average higher contents compared to pine bark, except for Pb and Cr.Size reduction of spruce and pine bark did not apply randomly to the different components and instead resulted into partial separation of the inorganic and organic matter into different size particles. Fine particles concentrated higher amounts of inorganic material and of extractives.     

Briarane Diterpenoids Isolated from Gorgonian Corals between 2011 and 2013

The structures, names, bioactivities and references of 138 briarane-type diterpenoids, including 87 new compounds, are summarized in this review. All the briarane-type compounds mentioned in this review article were obtained from gorgonian corals including the genus Briareum, Dichotella, Junceella and Verrucella. Some of these compounds showed potential bioactivities.     

二穗短柄草异戊烯基转移酶(IPT)编码基因的进化及功能分析

细胞分裂素(CTK)是一类重要的植物激素,主要作用是引起细胞分裂,诱导芽的形成和促进芽的生长。此外,CTK能够通过参与细胞分化来调控根分生组织大小,对根系生长有负调控作用。异戊烯基转移酶(IPT)是CTK合成过程中的一个关键的限速酶,在高等植物中均以多同源拷贝形式存在。为了探寻二穗短柄草IPT基因的进化起源,并阐明同源基因间潜在的功能分化及其在根系生长过程中的生物学功能,首先,对拟南芥及二穗短柄草的IPT基因进行了序列比对和进化分析,其次,利用荧光定量的方法对二穗短柄草中各IPT基因在不同组织不同发育阶段的转录水平进行了定量分析,最后,通过构建IPT基因RNAi的表达载体,对二穗短柄草中多个IPT基因的转录进行了沉默干扰。结果表明,tRNA-IPT可能代表了IPT祖先基因的功能,而且是ATP/ADP-IPT基因的供体基因。二穗短柄草各IPT基因具有一定的组织表达特异性,大部分ATP/ADP-IPTs处于转录不活跃状态,而tRNA-IPTs在根部和叶部的表达量都很高。因此,IPT基因在单子叶模式植物二穗短柄草中可能采用了不同于拟南芥的方式发挥功能,其主要的发挥功能形式是tRNA类型。二穗短柄草转IPT-RNAi植株表现出根系增强的表型,说明在根系早期发育阶段,二穗短柄草ATP/ADP型IPT基因起到了一定的调节作用。由于IPT基因在早熟禾亚科物种中较为保守,本研究可为增强麦类作物根系发育与提高抗旱性提供必要理论基础。     

Comparative Analysis of Glycoside Hydrolases Activities from Phylogenetically Diverse Marine Bacteria of the Genus Arenibacter

A total of 16 marine strains belonging to the genus Arenibacter, recovered from diverse microbial communities associated with various marine habitats and collected from different locations, were evaluated in degradation of natural polysaccharides and chromogenic glycosides. Most strains were affiliated with five recognized species, and some presented three new species within the genus Arenibacter. No strains contained enzymes depolymerizing polysaccharides, but synthesized a wide spectrum of glycosidases. Highly active β-N-acetylglucosaminidases and α-N-acetylgalactosaminidases were the main glycosidases for all Arenibacter. The genes, encoding two new members of glycoside hydrolyses (GH) families, 20 and 109, were isolated and characterized from the genomes of Arenibacter latericius. Molecular genetic analysis using glycosidase-specific primers shows the absence of GH27 and GH36 genes. A sequence comparison with functionally-characterized GH20 and GH109 enzymes shows that both sequences are closest to the enzymes of chitinolytic bacteria Vibrio furnissii and Cellulomonas fimi of marine and terrestrial origin, as well as human pathogen Elisabethkingia meningoseptica and simbionts Akkermansia muciniphila, gut and non-gut Bacteroides, respectively. These results revealed that the genus Arenibacter is a highly taxonomic diverse group of microorganisms, which can participate in degradation of natural polymers in marine environments depending on their niche and habitat adaptations. They are new prospective candidates for biotechnological applications due to their production of unique glycosidases.