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Journal of Biotechnology

Richa Sharma, Vijaylakshmi Jamwal, Varun P Singh, Priya Wazir, Praveen Awasthi, Deepika Singh, Sumit G Gandhi, Ram A Vishwakarma, Asha Chaubey
Streptomyces species are amongst the most exploited microorganisms due to their ability to produce a plethora of secondary metabolites with bioactive potential, including several well known drugs. They are endowed with immense unexplored potential and substantial efforts are required for their isolation as well as characterization for their bioactive potential. Unexplored niches and extreme environments are host to diverse microbial species. In this study, we report Streptomyces lavendulae ACR-DA1, isolated from extreme cold deserts of the North Western Himalayas, which produces a macrolactone antibiotic, valinomycin...
May 18, 2017: Journal of Biotechnology
Ruifang Liu, Yu Zhang, Ping Chen, Haiyan Lin, Guoyou Ye, Zhongwei Wang, Changwei Ge, Bo Zhu, Deyong Ren
Plant-microbe interactions can provide agronomic benefits, such as enhancing nutrient uptake and providing fixed nitrogen. The Pseudomonas psychrotolerans strain PRS08-11306 was isolated from rice seeds and can enhance plant growth. Here, we analyzed the P. psychrotolerans genome, which is ∼5Mb, with 4389 coding sequences, 77 tRNAs, and 7 rRNAs. Genome analysis identified a cluster of turnerbactin biosynthetic genes, which are responsible for the production of a catecholate siderophore and contribute to nitrogen fixation for the host...
May 18, 2017: Journal of Biotechnology
Rabeaa S Alkhateeb, Christian Rückert, Oliver Rupp, Boas Pucker, Gerd Hublik, Daniel Wibberg, Karsten Niehaus, Alfred Pühler, Frank-Jörg Vorhölter
Bioinformatics tools and gene expression data were applied to identify new genes and to enhance the accuracy in genomic feature predictions for Xanthomonas campestris pv. campestris B100, a pathogen of cruciferous plants and model strain for the biosynthesis of xanthan, a polysaccharide with a multitude of commercial applications as a thickening agent. Results from 5'-enriched RNA end-sequencing and total transcriptome RNA-seq experiments were used for this purpose. Functional gene annotations were updated where new evidence had emerged and start codon predictions were enhanced for 153 protein-coding genes (CDS)...
May 12, 2017: Journal of Biotechnology
Michał Banasik, Anna Stanisławska-Sachadyn, Ewa Hildebrandt, Paweł Sachadyn
The mismatch binding protein MutS is responsible for the recognition of mispaired and unpaired bases, which is the initial step in DNA repair. Among the MutS proteins most extensively studied in vitro are those derived from Thermus thermophilus, Thermus aquaticus and Escherichia coli. Here, we present the first report on the in vitro examination of DNA mismatch binding activity of MutS protein from Deinococcus radiodurans and confront this with the properties of those from E. coli and T. thermophilus. The analyses which included mobility gel-shift assay, colorimetric and qPCR estimation of MutS-bound DNA clearly showed that D...
May 12, 2017: Journal of Biotechnology
Jingjing Liu, Zhipeng Xie, Hyun-Dong Shin, Jianghua Li, Guocheng Du, Jian Chen, Long Liu
Aspergillus oryzae finds wide application in the food, feed, and wine industries, and is an excellent cell factory platform for production of organic acids. In this work, we achieved the overproduction of L-malate by rewiring the reductive tricarboxylic acid (rTCA) pathway and L-malate transport pathway of A. oryzae NRRL 3488. First, overexpression of native pyruvate carboxylase and malate dehydrogenase in the rTCA pathway improved the L-malate titer from 26.1gL(-1) to 42.3gL(-1) in shake flask culture. Then, the oxaloacetate anaplerotic reaction was constructed by heterologous expression of phosphoenolpyruvate carboxykinase and phosphoenolpyruvate carboxylase from Escherichia coli, increasing the L-malate titer to 58...
May 12, 2017: Journal of Biotechnology
Christian Rupprecht, Marcus Wingen, Janko Potzkei, Thomas Gensch, Karl-Erich Jaeger, Thomas Drepper
The intracellular pH is an important modulator of various bio(techno)logical processes such as enzymatic conversion of metabolites or transport across the cell membrane. Changes of intracellular pH due to altered proton distribution can thus cause dysfunction of cellular processes. Consequently, accurate monitoring of intracellular pH allows elucidating the pH-dependency of (patho)physiological and biotechnological processes. In this context, genetically encoded biosensors represent a powerful tool to determine intracellular pH values non-invasively and with high spatiotemporal resolution...
May 10, 2017: Journal of Biotechnology
Gunaseelan Dhanarajan, Vivek Rangarajan, Chandrakanth Bandi, Abhivyakti Dixit, Susmita Das, Kranthikiran Ale, Ramkrishna Sen
A lipopeptide biosurfactant produced by marine Bacillus megaterium and a biopolymer produced by thermophilic Bacillus licheniformis were tested for their application potential in the enhanced oil recovery. The crude biosurfactant obtained after acid precipitation effectively reduced the surface tension of deionized water from 70.5 to 28.25mN/m and the interfacial tension between lube oil and water from 18.6 to 1.5mN/m at a concentration of 250mgL(-1). The biosurfactant exhibited a maximum emulsification activity (E24) of 81...
May 10, 2017: Journal of Biotechnology
Axel von Kamp, Sven Thiele, Oliver Hädicke, Steffen Klamt
Mathematical models of the cellular metabolism have become an essential tool for the optimization of biotechnological processes. They help to obtain a systemic understanding of the metabolic processes in the used microorganisms and to find suitable genetic modifications maximizing the production performance. In particular, methods of stoichiometric and constraint-based modeling are frequently used in the context of metabolic and bioprocess engineering. Since metabolic networks can be complex and comprise hundreds or even thousands of metabolites and reactions, dedicated software tools are required for an efficient analysis...
May 9, 2017: Journal of Biotechnology
Ruud H Deurenberg, Erik Bathoorn, Monika A Chlebowicz, Natacha Couto, Mithila Ferdous, Silvia García-Cobos, Anna M D Kooistra-Smid, Erwin C Raangs, Sigrid Rosema, Alida C M Veloo, Kai Zhou, Alexander W Friedrich, John W A Rossen
Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test...
May 8, 2017: Journal of Biotechnology
Lorenz C Reimer, Carola Söhngen, Anna Vetcininova, Jörg Overmann
Microbial data and metadata are scattered throughout the scientific literature, databases and unpublished lab notes and thereby often are difficult to access. Hot spots of (meta)data are internal descriptions of culture collections and initial descriptions of novel taxa in primary literature. Here we describe three exemplary mobilization projects which yielded metadata published through the prokaryotic metadatabase BacDive. The Reichenbach collection of myxobacteria includes information on 12,535 typewritten index cards which were digitized...
May 6, 2017: Journal of Biotechnology
Wah-Seng See-Too, Kah-Ooi Chua, Yan-Lue Lim, Jian-Woon Chen, Peter Convey, Taznim Begam Mohd Mohidin, Wai-Fong Yin, Kok-Gan Chan
The type strain Planococcus donghaensis JH1(T) is a psychrotolerant and halotolerant bacterium with starch-degrading ability. Here, we determine the carbon utilization profile of P. donghaensis JH1(T) and report the first complete genome of the strain. This study revealed the strain's ability to utilize pectin and d-galacturonic acid, and identified genes responsible for degradation of the polysaccharides. The genomic information provided may serve as a fundamental resource for full exploration of the biotechnological potential of P...
May 5, 2017: Journal of Biotechnology
Wenchao Sun, Changzhan Xie, Cao Liang, Min Zheng, Guanyu Zhao, Ping Zhang, Jicheng Han, Jie Jing, Shubo Wen, Pengpeng Xiao, Zhuodong Cui, Jinyong Zhang, Jingqiang Ren, Hao Liu, Huijun Lu, Ningyi Jin
The Torque teno canis virus (TTCaV) is a small virus with circular single-stranded DNA that has been reported to cause infections in dogs. The present study aimed to identify the presence of TTCaV in blood samples obtained from domestic dogs, and examine its diversity and evolution of the genomes. Five strains of TTCaV were detected, and the overall prevalence was found to be 7% (28/400). Phylogenetic analysis showed that the five genomes were closely clustered with the previously known Cf-TTV10 and LDL strains and formed a Thetatorque virus...
May 5, 2017: Journal of Biotechnology
Gandhi Rádis-Baptista, Iana S Campelo, Jean-Étienne R L Morlighem, Luciana M Melo, Vicente J F Freitas
Cell-penetrating peptides (CPPs) have been studied for their capacity to translocate across the lipid membrane of several cell types. In membrane translocation, these peptides can remarkably transport biologically active hydrophilic molecules, such as pharmaceuticals, nucleic acids (DNA and RNA) and even high-molecular-weight proteins, Fig. 3 into the cell cytoplasm and organelles. The development of CPPs as transduction agents includes the modification of gene and protein expression, the reprogramming and differentiation of induced pluripotent stem cells and the preparation of cellular vaccines...
May 4, 2017: Journal of Biotechnology
Fernando Pérez-García, Christian Ziert, Joe Max Risse, Volker F Wendisch
The cyclic amino acid ectoine is a compatible solute serving as a protective substance against osmotic stress. Ectoine finds various applications due to its moisturizing effect. To avoid the disadvantages of the prevailing so-called "bacterial milking ectoine production process" caused by the high salt concentration, low salt fermentation strategies are sought after. As L-lysine and ectoine biosynthesis share L-aspartate-semialdehyde as common precursor, L-lysine producing strains can be converted to ectoine producing strains...
May 3, 2017: Journal of Biotechnology
Min Yin, Mingxing Jiang, Zhen Ren, Yilong Dong, Tao Lu
Streptomyces autolyticus CGMCC 0516 produces the anti-tumor benzoquinone ansamycins geldanamycin, autolytimycin, and reblastatin and the 16-membered macrodiolide elaiophylin. Here, we report the complete genome sequence of S. autolyticus CGMCC 0516, which consists of a 10,029,028bp linear chromosome and seven circular plasmids. Fifty-seven putative biosynthetic gene clusters for secondary metabolites were found. The geldanamycin, autolytimycin, and reblastatin biosynthetic gene clusters were located on the left arm (2...
May 2, 2017: Journal of Biotechnology
Alana Dreßen, Thomas Hilberath, Ursula Mackfeld, Jens Rudat, Martina Pohl
Phenylalanine ammonia lyase (PAL) from Arabidopsis thaliana (AtPAL2) is in general a very good catalyst for the amination of fluoro- and chloro-cinnamic acid derivatives yielding halogenated (S)-phenylalanine derivatives with ≥85% conversion and excellent ee values >99%. We have studied the application of this enzyme as whole cell biocatalyst and immobilized on the cellulose carrier Avicel(®) for the production of the hypertension drug precursor (S)-2-chloro-phenylalanine using batch, fed-batch, as well as continuous membrane reactor and plug-flow reactor...
May 1, 2017: Journal of Biotechnology
Da-Zhong Yan, Xin Li, Cun-Zhi Li, Ling-Qi Mao, Xiang-Qun Chi, Ning-Yi Zhou, Dong-Yan Liu
The Gram-negative strain of Pseudomonas plecoglossicida NyZ12 isolated from soil has the ability to degrade cyclohexylamine (CHAM). The genes encoding CHAM degradation by gram-negative bacteria, however, have not been reported previously. In this study, ORFs predicted to encode CHAM degradation by NyZ12 were identified by bioinformatics analysis. Differential expression of the proposed ORFs was analyzed via RNA-seq and quantitative reverse transcription-PCR (qRT-PCR), using RNA extracted from NyZ12 cultured with or without CHAM addition...
May 1, 2017: Journal of Biotechnology
Michel Oelschlägel, Lysann Richter, Anna Stuhr, Sarah Hofmann, Michael Schlömann
The styrene oxide isomerase (SOI, StyC) represents a key enzyme of the styrene-degrading pathway and has been discussed as promising biocatalyst during recent studies. The enzyme enables the synthesis of pure phenylacetaldehyde from styrene oxide. In this study the native as well as the corresponding codon-optimized genes of three different SOIs from Rhodococcus opacus 1CP (StyC-1CP), Sphingopyxis fribergensis Kp5.2 (StyC-Kp5.2), and Pseudomonas fluorescens ST (StyC-ST) were investigated for the expression in Escherichia coli BL21(DE3)pLysS...
May 1, 2017: Journal of Biotechnology
Jian Guo, Yuanhua Wang, Baozhong Li, Siyao Huang, Yefu Chen, Xuewu Guo, Dongguang Xiao
Aureobasidium pullulans is an increasingly attractive host for bio-production of pullulan, heavy oil, polymalic acid, and a large spectrum of extracellular enzymes. To date, genetic manipulation of A. pullulans mainly relies on time-consuming conventional restriction enzyme digestion and ligation methods. In this study, we present a one-step homologous recombination-based method for rapid genetic manipulation in A. pullulans. Overlaps measuring >40bp length and 10μg DNA segments for homologous recombination provided maximum benefits to transformation of A...
April 29, 2017: Journal of Biotechnology
Chen Zhao, Qi Gao, Jun Chen, Liujing Wei, Tadayuki Imanaka, Qiang Hua
The metabolomic studies were conducted for both the engineered lycopene-producing Yarrowia lipolytica strain and the control strain. The changes in metabolome profiling and main pathway abundance of Y. lipolytica with the introduction of heterologous crt genes were investigated by multiple analytical and statistical methods More importantly, the metabolome data were transformed into pathway abundances visualized by a pathway relationship network using Cytoscape software. This network provided a simple way to present the statistical results of pathway abundance and interpret the effects of the crt genes in a metabolic view, and the results highlighted the up-regulation of eight pathways and the down-regulation of three pathways in the lycopene fast production phase...
April 29, 2017: Journal of Biotechnology
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