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عنوان فارسی	بیان متفاوت ژن اوپرون mtr در مسیر انتقال الکترون خارج سلولی باکتری Shewanella oneidensis MR-۱ تحت شرایط محدودیت الکترون پذیرندگی

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عنوان انگلیسی	Differential gene expression of mtr operon in Shewanella oneidensis MR-1 extracellular electron transport pathway under electron acceptor limitation condition

چکیده انگلیسی مقاله	Objective and background Microbial fuel cells are bioenergy sources in which electricity is produced through anaerobic catalysis of organic matter using a biocatalyst. The current limitation of these systems is low power production that prevents them from being used as a viable source of energy. One of the most comprehensive solutions to overcome this limitation is genetic modification to enhance the extracellular electron transport in exoelectrogene bacteria such as Shewanella oneidensis MR-1. To embark on this modification, the genes involved in extracellular electron transport and their interactions need to be well understood in advance. One technique to identify those genes expressed in extracellular electron transport is their differential expression under perturbed environmental conditions. Barchinger et al. (2016) applied oxygen limitation to a Shewanella oneidensis MR-1chemostat culture and produced RNA-Seq data to obtain 50-bp single-end reads for the collected samples. The sequence data have been deposited in the Gene Expression Omnibus database under accession number GSE79964. In this work, using two gene expression data analysis softwares, SPARTA and Rockhopper, the RNA-Seq data was analyzed. In this analysis, the regulation of differentially expressed genes under oxygen limitation was investigated and the most regulated gene cluster in shifting from aerobic to anaerobic extracellular electron transport were identified. Methodology Data The raw gene expression data was retrieved from Gene Expression Omnibus database under accession number GSE79964. According to Barchinger et al. (2016), the RNA-Seq data is produced using samples collected from a chemostat that was subject to oxygen limitation at t=0 and four other time periods with 15 minutes interval up to 60 minutes from the oxygen limitation application. Collectively, the data is presented at times 0, 15, 30, 45, and 60 minutes after oxygen starvation. The raw data is originally in .sra format that was then converted to fastq format using SRAToolkit. Software Two gene expression data analysis softwares, SPARTA (version 1.0) and Rockhopper (version 2.0.3) were used in this study. These two softwares are specific to analyze bacterial genome RNA-Seq data. Results Analysis of gene expression profile of Shewanella oneidensis MR-1 using two different softwares SPARTA and Rockhopper revealed that 220 genes were differentially expressed when the culture condition underwent electron acceptor limitation. During this perturbation, the two analyzes agreed that 207 genes were up-regulated while 13 genes were down-regulated. Most of the over-expressed genes were those that express proteins responsible for adopting the change from aerobic respiration to anaerobic metabolism. Among those are four genes including mtrA, mtrB, mtrC, omcA that are clustered as Mtr operon and one single gene cymA that are collectively involved in extracellular electron transport mechanism. The cymA encodes CymA protein that is attached to the inner membrane. This protein is a tetraheme cytochrome with a large C-terminus in periplasmic space that facilitates the electron transfer to another decaheme cytochrome protein MtrA. The mtrB is encoding MtrB, a decaheme type c cytochrome protein that makes a stable complex with MtrA and MtrC. This protein is essential to localization and attachment of MtrC and OmcA to the outer surface of the cell. MtrC and OmcA are terminal reductases to transfer electrons to extracellular acceptors. The results indicated that immediately after oxygen limitation MtrC underwent the greatest over expression of 4.2-fold on average between Rockhopper (3.9) and SPARTA (4.5) analyzes. However, over the time course of 60 minutes of electron acceptor starvation, MtrB showed the greatest change in expression of 6.7-fold on average between Rockhopper (6.3) and SPARTA (7.1) results. Furthermore, OmcA and MtrC are both outer membrane cytochromes that play key roles in surface attachment and electron transfer to extracellular acceptors, respectively in direct contact mechanism. In anaerobic environment, however, nanowire formation is promoted and electron transfer becomes more important than surface attachment. Our results indicated that expression level of mtrC increased 18% more of omcA gene that confirms more important role of MtrC cytochrome than OmcA in limited electron acceptor condition. Over the time course of 60 minutes, expression level of mtrC was still higher than that of omcA but dropped to 12%. This indicates that this change in expression level take place immediately after oxygen limitation. Conclusions Gene expression analysis results revealed the key role of mtr operon in extracellular electron transport pathway in Shewanella oneidensis MR-1. Under electron acceptor limitation condition the genes clustered in this operon were up-regulated and the gene products were over-expressed. The level of expression varied from 4.2-fold to 6.7-fold among coordinated proteins. This indicated that mtr genes should be subject to any modification for the purpose of genetic engineering improvements.

کلیدواژه‌های انگلیسی مقاله	Extracellular electron transport، Differentially expressed genes، Mtr operon

نویسندگان مقاله	زهره خدادادی \| zohre khodadadi department of chemical engineering, ferdowsi university of mashhad, azadi square, pardis campus, 91779-48944, mashhad, iran گروه مهندسی شیمی، دانشگاه فردوسی مشهد، میدان آزادی، پردیس دانشگاه،91779-48944، مشهد، ایران سازمان اصلی تایید شده: دانشگاه فردوسی (Ferdowsi university) محمود اخوان مهدوی \| mahmood a mahdavi department of chemical engineering, ferdowsi university of mashhad, azadi square, pardis campus, 91779-48944, mashhad, iran گروه مهندسی شیمی، دانشگاه فردوسی مشهد، میدان آزادی، پردیس دانشگاه،91779-48944، مشهد، ایران سازمان اصلی تایید شده: دانشگاه فردوسی (Ferdowsi university) رضا قشلاقی \| reza gheshlaghi department of chemical engineering, ferdowsi university of mashhad, azadi square, pardis campus, 91779-48944, mashhad, iran گروه مهندسی شیمی، دانشگاه فردوسی مشهد، میدان آزادی، پردیس دانشگاه،91779-48944، مشهد، ایران سازمان اصلی تایید شده: دانشگاه فردوسی (Ferdowsi university)

نشانی اینترنتی	http://icsb2018.modares.ac.ir/browse.php?a_code=A-10-69-1&slc_lang=fa&sid=1
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