Applied Biochemistry and Biotechnology (v.177, #4)

The Chemical Diversity of the Ascomycete Fungus Paecilomyces variotii by Roberto Mioso; Francisco Javier Toledo Marante; Irma Herrera Bravo de Laguna (781-791).
Paecilomyces variotii isolated from a broad range of habitats drives the diversification of new high-value-added secondary metabolites that could potentially play an important role in human and animal health. These metabolites include the anhydride metabolite of the nonadride family, as well as the following compounds: naphthopyranone metabolites, sphingofungins, eicosenoic acids, new branched fatty acids, ascofuranone, polyketides, an anacardic acid analogue, straight-chain peptides, and volatile compounds. These natural products show that P. variotii can provide leading compounds for new drug discoveries, which may include herbicide agents, some of which are important in the agrochemical market. Finally, this review outlines recent developments, trends, and prospects for the chemistry of this ascomycete.
Keywords: Paecilomyces variotii ; Byssochlamys spectabilis ; Fungus; Secondary metabolites; Bioactive compounds

Cold stress, as chilling (<20 °C) or freezing (<0 °C), is one of the frequently exposed stresses in cultivated plants like potato. Under cold stress, plants differentially modulate their gene expression to develop a cold tolerance/acclimation. In the present study, we aimed to identify the overall gene expression profile of chilling-stressed (+4 °C) potato at four time points (4, 8, 12, and 48 h), with a particular emphasis on the genes related with transcription factors (TFs), phytohormones, lipid metabolism, signaling pathway, and photosynthesis. A total of 3504 differentially expressed genes (DEGs) were identified at four time points of chilling-induced potato, of which 1397 were found to be up-regulated while 2107 were down-regulated. Heatmap showed that genes were mainly up-regulated at 4-, 8-, and 12-h time points; however, at 48-h time point, they inclined to down-regulate. Seventy five up-regulated TF genes were identified from 37 different families/groups, including mainly from bHLH, WRKY, CCAAT-binding, HAP3, and bZIP families. Protein kinases and calcium were major signaling molecules in cold-induced signaling pathway. A collaborated regulation of phytohormones was observed in chilling-stressed potato. Lipid metabolisms were regulated in a way, highly probably, to change membrane composition to avoid cold damage and render in signaling. A down-regulated gene expression profile was observed in photosynthesis pathway, probably resulting from chilling-induced reduced enzyme activity or light-triggered ROSs damage. The findings of this study will be a valuable theoretical knowledge in terms of understanding the chilling-induced tolerance mechanisms in cultivated potato plants as well as in other Solanum species.
Keywords: Cold acclimation; COR genes; Phytohormone; Microarray; Signal transduction

Rhodium Complex and Enzyme Couple Mediated Electrochemical Detection of Adenosine by Dawoon Han; Hyeong-Mook Kim; Rohit Chand; Gyumin Kim; Ik-Soo Shin; Yong-Sang Kim (812-820).
Adenosine is one of the nucleoside which plays an important role in signal transduction and neuromodulation. This work proposes a simple electrochemical assay, comprising two enzymes and rhodium complex based electron transfer mediator, for the detection of adenosine. Sequential reaction of adenosine deaminase and l-glutamic dehydrogenase and the supporting cycle between β-NADH and mediator enable quantitative analysis of adenosine. Role of electron transfer mediator is the conveyance of proton from electrode to β-NAD+ for regeneration of β-NADH. The electrochemical characteristics of electron transfer mediator were also studied. Real-time adenosine detection was carried out using this multiple enzyme based chronoamperometric assay. The analysis results show a low limit of detection (140 μM) and good correspondence between current signal and the adenosine concentration (R 2 = 0.997).
Keywords: Adenosine; Enzymatic reaction; Electrochemical; Electron transfer mediator; Nafion

Application of a Label-Free Immunosensor for White Spot Syndrome Virus (WSSV) in Shrimp Cultivation Water by Thanyaporn Waiyapoka; Panchalika Deachamag; Wilaiwan Chotigeat; Nittaya Bunsanong; Proespichaya Kanatharana; Panote Thavarungkul; Suchera Loyprasert-Thananimit (821-830).
White spot syndrome virus (WSSV) is a major pathogen affecting the shrimp industry worldwide. In a preliminary study, WSSV binding protein (WBP) was specifically bound to the VP26 protein of WSSV. Therefore, we have developed the label-free affinity immunosensor using the WBP together with anti-GST-VP26 for quantitative detection of WSSV in shrimp pond water. When the biological molecules were immobilized on a gold electrode to form a self-assembled monolayer, it was then used to detect WSSV using a flow injection system with optimized conditions. Binding between the different copies of WSSV and the immobilized biological molecules was detected by an impedance change (ΔZ″) in real time. The sensitivity of the developed immunosensor was in the linear range of 1.6 × 101–1.6 × 106 copies/μl. The system was highly sensitive for the analysis of WSSV as shown by the lack of impedance change when using yellow head virus (YHV). The developed immunosensor could be reused up to 37 times (relative standard deviation (RSD), 3.24 %) with a good reproducibility of residual activity (80–110 %). The immunosensor was simple to operate, reliable, reproducible, and could be applied for the detection and quantification of WSSV in water during shrimp cultivation.
Keywords: White spot syndrome virus (WSSV); WSSV binding protein (WBP); Biosensor; Impedance; Label-free immunosensor; Shrimp cultivation

High-Level Butanol Production from Cassava Starch by a Newly Isolated Clostridium acetobutylicum by Shubo Li; Yuan Guo; Fuzhi Lu; Jiajian Huang; Zongwen Pang (831-841).
A new Clostridium acetobutylicum strain, exhibiting the ability to resist butanol stress and produce butanol, was identified and named GX01. Strain GX01 can use a wide variety of carbohydrates, especially cassava starch, to produce butanol. After the optimization of culture conditions, C. acetobutylicum GX01 could produce 27.3 g/L solvent, including 17.1 g/L butanol, 7.9 g/L acetone, and 2.3 g/L ethanol, from 100 g/L cassava flour and 3 g/L soybean meal. Furthermore, when its acetone-butanol-ethanol (ABE) fermentation was performed in 10- and 30-L bioreactors, the production of total solvent and butanol reached 29.2 and 18.3 g/L, respectively, and 28.8 and 18.8 g/L, respectively. Thus, the high level and stability of butanol production make strain GX01 a promising candidate for ABE fermentation using the low-cost cassava starch.
Keywords: Buatanol; Cassava starch; Clostridium acetobutylicum ; ABE fermentation

The present work for the first time investigates the effect of Bacillus amyloliquefaciens, M3, on a new poly(ether-urethane-urea) (PEUU). PEUU was synthesized via reaction of 4,4′-methylenebis(4-phenylisocyanate) (MDI), l-leucine anhydride cyclopeptide (LACP) as a degradable monomer and polyethylene glycol with molecular weight of 1000 (PEG-1000). Biodegradation of the synthesized PEUU as the only source for carbon and nitrogen for M3 was studied. The co-metabolism biodegradation of the polymer by this organism was also investigated by adding mannitol or nutrient broth to the basic media. Biodegradation of the synthesized polymer was followed by SEM, FT-IR, TGA, and XRD techniques. It was shown that incubation of PEUU with M3 resulted in a 30–44 % reduction in polymer’s weight after 1 month. This study indicates that the chemical structure of PEUU significantly changes after exposure to M3 due to hydrolytic and enzymatic degradation of polymer chains. The results of this work supports the idea that this poly(ether-urethane) is used as a sole carbon source by M3 and this bacterium has a good capability for degradation of poly(ether-urethane)s.
Keywords: Poly(ether-urethane-urea); Amino acid anhydride cyclopeptide; Bacillus amyloliquefaciens ; PEG; Biodegradation

Receptor-Guided De Novo Design of Dengue Envelope Protein Inhibitors by Vishal H. Desai; Sivakumar Prasanth Kumar; Himanshu A. Pandya; Hitesh A. Solanki (861-878).
Inhibitor design associated with the dynamics of dengue envelope protein at pre-fusion stage is a prominent strategy to interfere fusion transition of dengue virus with the host cell membrane. Receptor-guided de novo inhibitors were designed based on the knowledge of co-crystallized detergent, β-octyl glucoside. Pharmacophore features distribution showed the preference of aromatic groups with H bonding features connected to aliphatic bulky group as the skeleton for inhibitor design. Molecular dynamic simulations revealed (2R)-2-[(6-amino-1-oxohexan-2-yl)amino]-4-[6-(4-phenylpiperidine-1-yl)-1,2-benzoxazol-3-yl]butanoate as the probable binder which developed extensive conservative interactions despite the local pocket residues movements especially from kl β-hairpin, the key structural unit for initiating conformational changes required for fusion transition. The electronic and hydrophobic potentials also indicated that butanoate molecule as the initial lead for envelope protein inhibitors.
Keywords: Dengue envelope; De novo design; Envelope inhibitors; Docking; Pharmacophore; Dynamic simulations

New Insights on Coffea miRNAs: Features and Evolutionary Conservation by S. S. Chaves; C. N. Fernandes-Brum; G. F. F. Silva; B. C. Ferrara-Barbosa; L. V. Paiva; F. T. S. Nogueira; T. C. S. Cardoso; L. R. Amaral; M. de Souza Gomes; A. Chalfun-Junior (879-908).
Small RNAs influence the gene expression at the post-transcriptional level by guiding messenger RNA (mRNA) cleavage, translational repression, and chromatin modifications. In addition to model plants, the microRNAs (miRNAs) have been identified in different crop species. In this work, we developed a specific pipeline to search for coffee miRNA homologs on expressed sequence tags (ESTs) and genome survey sequences (GSS) databases. As a result, 36 microRNAs were identified and a total of 616 and 362 potential targets for Coffea arabica and Coffea canephora, respectively. The evolutionary analyses of these molecules were performed by comparing the primary and secondary structures of precursors and mature miRNAs with their orthologs. Moreover, using a stem-loop RT-PCR assay, we evaluated the accumulation of mature miRNAs in genomes with different ploidy levels, detecting an increase in the miRNAs accumulation according to the ploidy raising. Finally, a 5′ RACE (Rapid Amplification of cDNA Ends) assay was performed to verify the regulation of auxin responsive factor 8 (ARF8) by MIR167 in coffee plants. The great variety of target genes indicates the functional plasticity of these molecules and reinforces the importance of understanding the RNAi-dependent regulatory mechanisms. Our results expand the study of miRNAs and their target genes in this crop, providing new challenges to understand the biology of these species.
Keywords: Coffee; MicroRNAs; Evolutionary conservation; Stem-loop RT-PCR; 5′ RACE; PsRNATarget

Plantaricins, one of bacteriocin produced by Lactobacillus plantarum, are already known to have activities against several pathogenic bacterium. L. plantarum U10 isolated from “tempoyak,” an Indonesian fermented food, produced one kind of plantaricin designated as plantaricin W (plnW). The plnW is suggested as a putative membrane location of protein and has similar conserved motif which is important as immunity to bacteriocin itself. Thus, due to study about this plantaricin, several constructs have been cloned and protein was analyzed in Lactococcus lactis. In this study, plnW gene was successfully cloned into vector NICE system pNZ8148 and created the transformant named L. lactis NZ3900 pNZ8148-WU10. PlnW protein was 25.3 kDa in size. The concentration of expressed protein was significantly increased by 10 ng/mL nisin induction. Furthermore, PlnW exhibited protease activity with value of 2.22 ± 0.05 U/mL and specific activity about 1.65 ± 0.03 U/mg protein with 50 ng/mL nisin induction. Immunity study showed that the PlnW had immunity activity especially against plantaricin and rendered L. lactis recombinant an immunity broadly to other bacteriocins such as pediocin, fermentcin, and acidocin.
Keywords: Plantaricin; PlnW; pNZ8148; L. lactis ; Immunity

Diversity of Lactobacillus reuteri Strains in Converting Glycerol into 3-Hydroxypropionic Acid by G. Burgé; C. Saulou-Bérion; M. Moussa; B. Pollet; A. Flourat; F. Allais; V. Athès; H.E. Spinnler (923-939).
The present study aims at comparing the performances of three Lactobacillus reuteri strains (DSM 20016, DSM 17938, and ATCC 53608) in producing 3-hydroxypropionic acid (3-HP) from glycerol and at exploring inhibition phenomena during this bioconversion. Differences were highlighted between the three strains in terms of 3-HP production yield, kinetics of substrate consumption, and metabolite production. With a maximal productivity in non-optimal conditions (free pH) around 2 g.L−1.h−1 of 3-HP and 4 g.L−1.h−1 of 3-hydroxypropionaldehyde (3-HPA) depending on the strain, this study confirmed the potential of L. reuteri for the biotechnological production of 3-HP. Moreover, the molar ratios of 3-HP to 1,3-propanediol (1,3-PDO) obtained for the three strains (comprised between 1.25 and 1.65) showed systematically a higher 3-HP production. From these results, the DSM 17938 strain appeared to be the most promising strain. The impact of glycerol bioconversion on the bacteria’s physiological state (a decrease of around 40 % in DSM 17938 cells showing an enzymatic activity after 3 h) and survival (total loss of cultivability after 2 or 3 h depending on the strains) was revealed and discussed. The effect of each metabolite on L. reuteri DSM 17938 was further investigated, displaying a drastic inhibition caused by 3-HPA, while 3-HP induced lower impact and only at acidic pH.
Keywords: 3-Hydroxypropionic acid; Lactobacillus reuteri ; Glycerol bioconversion; Inhibitory activity

HN Protein of Newcastle Disease Virus Induces Apoptosis Through SAPK/JNK Pathway by R. S. Rajmani; Ravi Kumar Gandham; Shishir Kumar Gupta; A. P. Sahoo; Prafull Kumar Singh; Rajiv Kumar; Shikha Saxena; Uttara Chaturvedi; Ashok K. Tiwari (940-956).
Many viral proteins are responsible for causing induction of apoptosis in the target cells. Hemagglutinin neuraminidase (HN), a multifunctional protein of Newcastle disease virus (NDV), is one of such proteins. The present study was undertaken to determine the apoptotic potential of the HN gene in cultured human cervical cancer cell line (HeLa cell) and to elucidate the molecular mechanisms involved. The results of the study indicate that HN protein causes apoptosis in HeLa cells, as observed by the translocation of Phosphatidylserine, activation of caspases, cleavage of poly (ADP-ribose) polymerase (PARP), and DNA fragmentation. Further, we report that expression of HN protein upregulates the SAPK/JNK pathway leading to transactivation of c-Jun which in turn activates apoptosis signaling. The results of our study provide an insight into the mechanism through which HN induces apoptosis.
Keywords: Heamagglutinin neuraminidase (HN); Apoptosis; SAPK/JNK pathway; Caspases; NDV; Interferon-α (IFN-α); c-Jun

Human and Tree Shrew Alpha-synuclein: Comparative cDNA Sequence and Protein Structure Analysis by Zheng -Cun Wu; Zhang-Qiong Huang; Qin-Fang Jiang; Jie-jie Dai; Ying Zhang; Jia-Hong Gao; Xiao-Mei Sun; Nai-Hong Chen; Yu-He Yuan; Cong Li; Yuan-Yuan Han; Yun Li; Kai-Li Ma (957-966).
The synaptic protein alpha-synuclein (α-syn) is associated with a number of neurodegenerative diseases, and homology analyses among many species have been reported. Nevertheless, little is known about the cDNA sequence and protein structure of α-syn in tree shrews, and this information might contribute to our understanding of its role in both health and disease. We designed primers to the human α-syn cDNA sequence; then, tree shrew α-syn cDNA was obtained by RT-PCR and sequenced. Based on the acquired tree shrew α-syn cDNA sequence, both the amino acid sequence and the spatial structure of α-syn were predicted and analyzed. The homology analysis results showed that the tree shrew cDNA sequence matches the human cDNA sequence exactly except at nucleotide positions 45, 60, 65, 69, 93, 114, 147, 150, 157, 204, 252, 270, 284, 298, 308, and 324. Further protein sequence analysis revealed that the tree shrew α-syn protein sequence is 97.1 % identical to that of human α-syn. The secondary protein structure of tree shrew α-syn based on random coils and α-helices is the same as that of the human structure. The phosphorylation sites are highly conserved, except the site at position 103 of tree shrewα-syn. The predicted spatial structure of tree shrew α-syn is identical to that of human α-syn. Thus, α-syn might have a similar function in tree shrew and in human, and tree shrew might be a potential animal model for studying the pathogenesis of α-synucleinopathies.
Keywords: Alpha-synuclein; Tree shrew; cDNA; Protein structure

Candida rugosa Lipase Immobilized onto Acid-Functionalized Multi-walled Carbon Nanotubes for Sustainable Production of Methyl Oleate by Nur Haziqah Che Marzuki; Naji Arafat Mahat; Fahrul Huyop; Nor Aziah Buang; Roswanira Abdul Wahab (967-984).
The chemical production of methyl oleate using chemically synthesized fatty acid alcohols and other toxic chemicals may lead to significant environmental hazards to mankind. Being a highly valuable fatty acid replacement raw material in oleochemical industry, the mass production of methyl oleate via environmentally favorable processes is of concern. In this context, an alternative technique utilizing Candida rugosa lipase (CRL) physically adsorbed on multi-walled carbon nanotubes (MWCNTs) has been suggested. In this study, the acid-functionalized MWCNTs prepared using a mixture of HNO3 and H2SO4 (1:3 v/v) was used as support for immobilizing CRL onto MWCNTs (CRL–MWCNTs) as biocatalysts. Enzymatic esterification was performed and the efficiency of CRL–MWCNTs was evaluated against the free CRL under varying conditions, viz. temperature, molar ratio of acid/alcohol, solvent log P, and enzyme loading. The CRL–MWCNTs resulted in 30–110 % improvement in the production of methyl oleate over the free CRL. The CRL–MWCNTs attained its highest yield (84.17 %) at 50 °C, molar ratio of acid/alcohol of 1:3, 3 mg/mL of enzyme loading, and iso-octane (log P 4.5) as solvent. Consequently, physical adsorption of CRL onto acid-functionalized MWCNTs has improved the activity and stability of CRL and hence provides an environmentally friendly means for the production of methyl oleate.
Keywords: Multi-walled carbon nanotubes; Candida rugosa lipase; Immobilization; Esterification; Methyl oleate

Kinetics of Methane Production from Swine Manure and Buffalo Manure by Chen Sun; Weixing Cao; Ronghou Liu (985-995).
The degradation kinetics of swine and buffalo manure for methane production was investigated. Six kinetic models were employed to describe the corresponding experimental data. These models were evaluated by two statistical measurements, which were root mean square prediction error (RMSPE) and Akaike’s information criterion (AIC). The results showed that the logistic and Fitzhugh models could predict the experimental data very well for the digestion of swine and buffalo manure, respectively. The predicted methane yield potential for swine and buffalo manure was 487.9 and 340.4 mL CH4/g volatile solid (VS), respectively, which was close to experimental values, when the digestion temperature was 36 ± 1 °C in the biochemical methane potential assays. Besides, the rate constant revealed that swine manure had a much faster methane production rate than buffalo manure.
Keywords: Anaerobic digestion; Methane; Manure; Kinetics; Mesophilic digestion; Model

Solvents Production from a Mixture of Glucose and Xylose by Mixed Fermentation of Clostridium acetobutylicum and Saccharomyces cerevisiae by Gao-Xiang Qi; Lian Xiong; Chao Huang; Xue-Fang Chen; Xiao-Qing Lin; Xin-De Chen (996-1002).
To overcome the xylose utilization defect in ethanol fermentation by wide-type Saccharomyces cerevisiae and alleviate the carbon catabolite repression (CCR) in acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum, a novel mixed fermentation of S. cerevisiae and C. acetobutylicum was developed. When S. cerevisiae was inoculated 24 h earlier than C. acetobutylicum CH02, a higher solvents yield was achieved with 0.41 g/g, compared to 0.38 g/g in ABE fermentation, and when S. cerevisiae and C. acetobutylicum CH02 were inoculated simultaneously, a higher productivity was achieved with 0.32 g/L/h, compared to 0.15 g/L/h in ABE fermentation. The total solvents yield was improved by the high ethanol yield from glucose. The CCR in mixed fermentation was alleviated when glucose was utilized quickly by S. cerevisiae, and therefore, the productivity was improved. This study suggests that mixed fermentation is an effective solvents production method from a mixture of glucose and xylose.
Keywords: Mixed sugars; Ethanol fermentation; ABE fermentation; Carbon catabolite repression; Mixed fermentation