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Item type:Publication, Access status: without files , Orthogonal Information Encoding in Living Cells with High Error-Tolerance, Safety, and Fidelity(2018-03-16); Information encoding in DNA is of great interest but its applications in vivo might be questionable since errors could be enriched exponentially by cellular replications and the artificial sequences may interfere with the natural ones. Here, a novel self-error-detecting, three-base block encoding scheme (SED3B) is proposed for reliable and orthogonal information encoding in living cells. SED3B utilizes a novel way to add error detecting bases in small data blocks which can combine with the inherent redundancy of DNA molecules for effective error correction. Errors at a rate of 19% can be corrected as shown by error-prone PCR experiments with E. coli cells. Calculations based on this preliminary result show that SED3B encoded information in E. coli can be reliable for more than 12 000 years of continuous replication. Importantly, SED3B encoded sequences do not share sequence space to all reported natural DNA sequences except for some short tandem repeats, indicating a low biological relevance of encoded sequences for the first time. These features make SED3B attractive for broad orthogonal information encoding purposes in living cells, for example, comments/barcodes encoding in synthetic biology. For proof of concept, 10 different barcodes were encoded in E. coli cells. After continuous replications for 10 days including exposure to ultraviolet for 2-3 min (lethality >60%) per day, all barcodes were fully recovered, proving the stability of the encoded information. An online encoding-decoding system is implemented and available at http://biosystem.bt1.tu-harburg.de/sed3b/ .Publicationtype: Journal Article132 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Analysis and engineering of biomolecules and microorganisms: from genome-scale study of pathogens to programming of DNA and cells(2018); This thesis is consisted of three major but different parts with the general aims of systems level evaluation and engineering of biomolecules and biological systems. In the first part of this thesis, comparative genomic studies of mutans streptococci strains, which are involved in the development of dental caries, were performed for better understanding their pathogenicity at the level of systems biology. A mosaic-like structure of genome arrangement was revealed by genome alignment analysis. Genes related to pathogenicity were found to have high variations among the strains, whereas genes for oxidative stress resistance are well conserved, indicating the importance of this trait in the dental biofilm community. Genome-scale metabolic network analysis revealed significant differences in 42 pathways. A striking dissimilarity is the unique presence of two lactate oxidases in S. sobrinus DSM 20742, probably indicating an unusual capability of this strain in producing H2O2 and expanding its ecological niche. In addition, lactate oxidases may form a unique energy-producing pathway with other enzymes in S. sobrinus DSM 20742 that can remedy its deficiency in citrate utilization pathway. An "open" pan-genome was inferred by pan-genome analysis using 67 S. mutans genomes currently available including the strains sequenced in this study. An online regulation database for S. mutans, named StrepReg, was constructed by integrating a transcription factor-based gene regulatory network, which was derived from time-series transcriptome analysis, with STRING protein-protein interaction information and KEGG pathway information (http://biosystem.bt1.tu-harburg.de:1555/homes/). Although systems biology is a powerful tool in understanding the system level behaviors of biological systems, the establishment of predictive, multiscale models in systems biology is still a challenge due to the complexity of biological systems. For the same reason, mathematical models often fail in applications under physiological conditions, such as for identification of targets in metabolic engineering for the development of highly production strains. In the second part of this thesis, a novel multiple input-output (I/O) system was therefore proposed and verified, which allows the identification of limiting bioreactions or key enzymes in metabolic pathways and even the optimization of biomolecules in vivo. The basic idea is to design a multiple I/O system which can introduce various genetic manipulations (perturbations) into the cells and record the specific intracellular signal changes correspondingly. This was achieved by engineering the interactions of phage with E. coli cells. Specifically, a multiple I/O system was implemented using M13 phage derivatives which can introduce various perturbations into E. coli cells after infection, such as up- or down-regulation of specific gene expressions. Using a rationally designed biological circuit, the intracellular signal changes after introduction of the perturbations by the phage infection were linked to the phage reproduction process. This means, signal changes caused by specific perturbations are linked to the specific populations of phages introducing the corresponding perturbations. In this way, the various signals are ‘recorded’ in forms of corresponding populations of phage derivatives. The usefulness of the multiple I/O system was demonstrated with three applications, i.e. identification of beneficial genetic manipulations, parallel evaluation of various designs of enzymes, and parallel screening of key enzymes for L-lysine biosynthesis in E. coli. Various gene operations related or not related to L-lysine biosynthesis in E. coli were used as inputs and the intracellular lysine concentration changes were used to trigger output signals. Correct predictions of beneficial genetic manipulations for enhanced lysine production in E. coli were achieved. New and effective variants of a key enzyme aspartate kinase III (AK-III), which is strictly inhibited by L-lysine, were obtained and evaluated in parallel. Importantly, the I/O system shows a ultra-sensitivity in capturing signal changes caused by the certain perturbations introduced. The approach developed in this work opens up new possibilities in systems metabolic engineering and synthetic biology of industrial microorganisms for practical applications. In the third part of this thesis, a novel self-error-detecting, three-base block encoding scheme (SED3B), which takes full advantage of the inherent redundancy feature of DNA synthesis for error correction, was proposed for reliable information encoding in DNA of living cells. In addition to the high error tolerance, SED3B encoded sequences were shown to be orthogonal to natural DNA sequences, indicating for the first time a low biological relevance of the encoded sequences. Features such as effective error tolerance and low biological relevance make SED3B an appealing solution for orthogonal information encoding in living cells with low or no affections to their biological functions, e.g. as a comment language in programming cells in vivo and for biological barcode encoding. Based on error-prone PCR experiments it was estimated that more than 12,000 years of continuous replication would be required to make the SED3B encoded information in E. coli cells become unrecoverable. To facilitate the usage of SED3B as a comment and barcode encoding system in synthetic biology, an online encoding-decoding system was implemented and released at http://biosystem.bt1.tu-harburg.de/sed3b. In principle, SED3B is also applicable for in vitro large data storage in synthesized DNA. Although further investigation is required, preliminary analysis shows that SED3B has a great potential for increasing the storage density to over several exabytes (EBs) per gram DNA which is theoretically much higher than that of methods reported in literature so far.Publicationtype: Doctoral Thesis460 1266 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Engineering 'cell robots' for parallel and highly sensitive screening of biomolecules under in vivo conditionsCells are capable of rapid replication and performing tasks adaptively and ultra-sensitively and can be considered as cheap "biological-robots". Here we propose to engineer cells for screening biomolecules in parallel and with high sensitivity. Specifically, we place the biomolecule variants (library) on the bacterial phage M13. We then design cells to screen the library based on cell-phage interactions mediated by a specific intracellular signal change caused by the biomolecule of interest. For proof of concept, we used intracellular lysine concentration in E. coli as a signal to successfully screen variants of functional aspartate kinase III (AK-III) under in vivo conditions, a key enzyme in L-lysine biosynthesis which is strictly inhibited by L-lysine. Comparative studies with flow cytometry method failed to distinguish the wild-type from lysine resistance variants of AK-III, confirming a higher sensitivity of the method. It opens up a new and effective way of in vivo high-throughput screening for functional molecules and can be easily implemented at low costs.Publicationtype: Journal ArticleScopus© Citations 5 369 481 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , A novel, ultra-sensitive multiple input-output system for target identification in systems metabolic engineering of E. coli(2016-06-28)Publicationtype: Conference Poster not in Proceedings48 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Genome sequence of bacillus coagulans P38, an efficient polymer-grade l-lactate producer from cellulosic substrates(American Society for Microbiology, 2015-05-21); ; ; ; Bacillus coagulans P38 is an efficient polymer-grade l-lactic acid producer from a cellulosic carbon source. Here, the draft 3.37-Mb genome sequence of this potential strain may provide useful information to further improve the strain performance for higher titers and, importantly, to understand the mechanism of its high tolerance for 2-furfural.Publicationtype: Journal ArticleScopus© Citations 3 303 191 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Comparing the cariogenic species Streptococcus sobrinus and S. mutans on whole genome level(Co-Action Publishing, 2014-12-03); ; ; ; Background: Two closely related species of mutans streptococci, namely Streptococcus mutans and Streptococcus sobrinus, are associated with dental caries in humans. Their acidogenic and aciduric capacity is directly associated with the cariogenic potential of these bacteria. To survive acidic and temporarily harsh conditions in the human oral cavity with hundreds of other microbial co-colonizers as competitors, both species have developed numerous mechanisms for adaptation. Objectives: The recently published novel genome information for both species is used to elucidate genetic similarities but especially differences and to discuss the impact on cariogenicity of the corresponding phenotypic properties including adhesion, carbohydrate uptake and fermentation, acid tolerance, signaling by two component systems, competence, and oxidative stress resistance. Conclusions: S. sobrinus can down-regulate the SpaA-mediated adherence to the pellicle. It has a smaller number of two-component signaling systems and bacteriocin-related genes than S. mutans, but all or even more immunity proteins. It lacks the central competence genes comC, comS, and comR. There are more genes coding for glucosyltransferases and a novel energy production pathway formed by lactate oxidase, which is not found in S. mutans. Both species show considerable differences in the regulation of fructan catabolism. However, both S. mutans and S. sobrinus share most of these traits and should therefore be considered as equally virulent with regard to dental caries.Publicationtype: Journal ArticleScopus© Citations 67 159 205 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Genome sequence of type strain Paenibacillus polymyxa DSM 365, a highly efficient producer of optically active (R,R)-2,3-butanediolPaenibacillus polymyxa DSM 365, an efficient producer of (R,. R)-2,3-butanediol, is known to show the highest production titer and productivity reported to date. Here, the first draft genome sequence of this promising strain may provide the genetic basis for further insights into the molecular mechanisms underlying the production of (R,. R)-2,3-butanediol with high optical purity and at a high titer. It will also facilitate the design of rational strategies for further strain improvements, as well as construction of artificial biosynthetic pathways through synthetic biology for asymmetric synthesis of chiral 2,3-butanediol or acetoin in common microbial hosts.Publicationtype: Journal ArticleScopus© Citations 21 32 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Genome sequence of Tumebacillus flagellatus GST4, the first genome sequence of a species in the genus Tumebacillus(American Society for Microbiology, 2014); ; ; ; © 2014 Wang et al. We present here the first genome sequence of a species in the genus Tumebacillus. The draft genome sequence of Tumebacillus flagellatus GST4 provides a genetic basis for future studies addressing the origins, evolution, and ecological role of Tumebacillus organisms, as well as a source of acid-resistant amylase-encoding genes for further studies.Publicationtype: Journal ArticleScopus© Citations 3 127 143 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , 3DScapeCS : application of three dimensional, parallel, dynamic network visualization in CytoscapeBackground: The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux, demands an efficient way for better visualization and interpretation beyond the conventional, two-dimensional visualization tools.Results: We developed a 3D Cytoscape Client/Server (3DScapeCS) plugin, which adopted Cytoscape in interpreting different types of data, and UbiGraph for three-dimensional visualization. The extra dimension is useful in accommodating, visualizing, and distinguishing large-scale networks with multiple crossed connections in five case studies.Conclusions: Evaluation on several experimental data using 3DScapeCS and its special features, including multilevel graph layout, time-course data animation, and parallel visualization has proven its usefulness in visualizing complex data and help to make insightful conclusions.Publicationtype: Journal ArticleScopus© Citations 12 278 312 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Draft genome sequence of Lactococcus lactis subsp. lactis strain YF11(American Society for Microbiology, 2013-08-08); ; ; ; © 2013 Du et al. Lactococcus lactis subsp. lactis strain YF11 is a food preservative bacterium with a high capacity to produce nisin. Here, we announce the draft genome sequence of Lactococcus lactis subsp. lactis YF11 (2,527,433 bp with a G+C content of 34.81%).Publicationtype: Journal ArticleScopus© Citations 6 218 223