Genomic analysis reveals the biotechnological and industrial potential of levan producing halophilic extremophile, Halomonas smyrnensis AAD6T

Diken, Elif; Özer, Tuğba; Arıkan, Muzaffer; Emrence, Zeliha; Öner, Ebru Toksoy; Ustek, Duran; Arğa, Kazım Yalçın

doi:10.1186/s40064-015-1184-3

Cited by 39 publications

(23 citation statements)

References 48 publications

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“…elongata . All metabolic reconstructions of Halomonadaceae presented so far [43, 44] have assigned ATP specificity to the phosphofructokinase. However, the protein Helo_2186, which is annotated as 6-phosphofructokinase, shares only 30% similarity or less to experimentally characterized phosphofructokinases from bacteria such as E .…”

Section: Resultsmentioning

confidence: 99%

Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology

et al. 2017

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Halophilic bacteria use a variety of osmoregulatory methods, such as the accumulation of one or more compatible solutes. The wide diversity of compounds that can act as compatible solute complicates the task of understanding the different strategies that halophilic bacteria use to cope with salt. This is specially challenging when attempting to go beyond the pathway that produces a certain compatible solute towards an understanding of how the metabolic network as a whole addresses the problem. Metabolic reconstruction based on genomic data together with Flux Balance Analysis (FBA) is a promising tool to gain insight into this problem. However, as more of these reconstructions become available, it becomes clear that processes predicted by genome annotation may not reflect the processes that are active in vivo. As a case in point, E. coli is unable to grow aerobically on citrate in spite of having all the necessary genes to do it. It has also been shown that the realization of this genetic potential into an actual capability to metabolize citrate is an extremely unlikely event under normal evolutionary conditions. Moreover, many marine bacteria seem to have the same pathways to metabolize glucose but each species uses a different one. In this work, a metabolic network inferred from genomic annotation of the halophilic bacterium Halomonas elongata and proteomic profiling experiments are used as a starting point to motivate targeted experiments in order to find out some of the defining features of the osmoregulatory strategies of this bacterium. This new information is then used to refine the network in order to describe the actual capabilities of H. elongata, rather than its genetic potential.

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Section: Resultsmentioning

confidence: 99%

Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology

et al. 2017

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“…Recently, Diken et al ( 2015 ) performed the whole-genome analysis of H. smyrnensis AAD6 T to investigate biological mechanisms, and furthermore, the genome-scale metabolic model i KYA1142, which included 980 metabolites and 1142 metabolic reactions, was reconstructed. The genomic analysis figured out the biotechnological potential of this microorganism as a result of its capacity to produce levan, Pel exopolysaccharide, polyhydroxyalkanoates (PHA), and osmoprotectants.…”

Section: Levanmentioning

confidence: 99%

Systems Biology of Microbial Exopolysaccharides Production

Ateş

2015

Front. Bioeng. Biotechnol.

214

110

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Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.

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“…The genome-scale cell model is a great tool to design and reform strategies to alter cell properties (Hong 2012;Lu et al 2014;Basler 2015;Diken et al 2015;Imam et al 2015;Kavscek et al 2015;King et al 2015;Parambil and Sarkar 2015). Bioinformatic tools for digging genome data and system-biology approaches contribute to the research of metabolic engineering (Nielsen and Jewett 2008) such as MetaFluxNet (Sang et al 2005) and TICL tool (Alexey et al 2009).…”

Section: Bioinformatics Tools and Omics Data Contribute To Design Metmentioning

confidence: 99%

Heterologous biosynthesis of artemisinic acid in Saccharomyces cerevisiae

Wang

et al. 2016

J Appl Microbiol

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Summary Artemisinic acid is a precursor of antimalarial compound artemisinin. The titre of biosynthesis of artemisinic acid using Saccharomyces cerevisiae platform has been achieved up to 25 g l−1; however, the performance of platform cells is still industrial unsatisfied. Many strategies have been proposed to improve the titre of artemisinic acid. The traditional strategies mainly focused on partial target sites, simple up‐regulation key genes or repression competing pathways in the total synthesis route. However, this may result in unbalance of carbon fluxes and dysfunction of metabolism. In this review, the recent advances on the promising methods in silico and in vivo for biosynthesis of artemisinic acid have been discussed. The bioinformatics and omics techniques have brought a great prospect for improving production of artemisinin and other pharmacal compounds in heterologous platform.

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Genomic analysis reveals the biotechnological and industrial potential of levan producing halophilic extremophile, Halomonas smyrnensis AAD6T

Cited by 39 publications

References 48 publications

Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology

Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology

Systems Biology of Microbial Exopolysaccharides Production

Heterologous biosynthesis of artemisinic acid in Saccharomyces cerevisiae

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