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بازسازی و آنالیز شبکه متابولیکی مبتنی بر ژنوم باکتری استرپتوکوکوس بویس B315 دخیل در تولید اسید لاکتیک در محیط شکمبه | ||
| علوم دامی | ||
| مقاله 9، دوره 31، شماره 121، اسفند 1397، صفحه 103-116 اصل مقاله (1.15 M) | ||
| نوع مقاله: مقاله پژوهشی | ||
| شناسه دیجیتال (DOI): 10.22092/asj.2018.116808.1595 | ||
| نویسندگان | ||
| صابر جلوخانی نیارکی* 1؛ مجتبی طهمورث پور2؛ زرین مینوچهر3؛ احسان معتمدیان4؛ محمدرضا نصیری2 | ||
| 1دانش آموخته دکتری، گروه علوم دامی، دانشکده کشاورزی، دانشگاه فردوسی مشهد | ||
| 2استاد، گروه علوم دامی، دانشکده کشاورزی، دانشگاه فردوسی مشهد | ||
| 3دانشیار، گروه زیست فناوری سامانه ای، پژوهشگاه ملی مهندسی ژنتیک و زیست فناوری، تهران | ||
| 4استادیار، گروه بیوتکنولوژی، دانشکده مهندسی شیمی، دانشگاه تربیت مدرس، تهران | ||
| چکیده | ||
| استرپتوکوکوس بویس یکی از باکتری های مصرف کننده نشاسته و تولیدکننده اسید لاکتیک در شکمبه است. با توجه به نقش استرپتوکوکوس بویس در تولید اسید لاکتیک، اطلاعات زیستی وسیعی از این گونه منتشر شده است. اما تا به حال، خصوصیات و توانمندی های متابولیکی این باکتری در سطح یک سیستم تجزیه و تحلیل نشده است. در پژوهش حاضر، مدل متابولیکی مبتنی بر ژنوم باکتری استرپتوکوکوس بویس (iStr472) برای اولین بار بر اساس اطلاعات ژنومی بدست آمده از سویه استرپتوکوکوس بویس B315 ساخته شد. مدل iStr472 با اهداف مختلف نظیر استواری، توپولوژی و توانایی های مدل در مصرف سوبستراهای دیگر آنالیز گردید. مدل بازسازی شده تعداد 694 واکنش، 626 متابولیت و 472 ژن را شامل گردید. بیشترین واکنش ها در مسیر متابولیکی نوکلئوتیدها قرار داشتند. ژن های متابولیکی مدل 6/27 درصد از کل ژن های رمزگذارنده را شامل شد. مقایسه دو مدل (iStr472 و ModelSEED) نشان داد که مدل iStr472 از دقت و صحت بالاتری نسبت به مدل دیگر برخوردار است. شانزده متابولیت با درجه اتصال بالا در مدل شناسایی گردید. حذف واکنش ها نشان داد که مدل 126 واکنش حیاتی برای رشد را شامل می شود. بر اساس پیش بینی مدل، تولید زیست توده استرپتوکوکوس بویس تحت تأثیر لاکتات تولیدی قرار می گیرد. مدل همچنین قادر است از فروکتوز به عنوان منبع کربنی استفاده کند. روی هم رفته، از پیش بینی های مدل iStr472 می توان به عنوان ابزاری برای درک بهتر متابولیسم و همچنین مهندسی متابولیک استرپتوکوکوس بویس به منظور تولید لاکتات کمتر در محیط شکمبه بهره برد. | ||
| کلیدواژهها | ||
| استرپتوکوکوس بویس؛ مدل متابولیکی مبتنی بر ژنوم؛ iStr472؛ شکمبه؛ COBRA | ||
| عنوان مقاله [English] | ||
| Reconstruction and analysis of the genome-scale metabolic network of Streptococcus bovis B315 involved in lactic acid production in the rumen | ||
| نویسندگان [English] | ||
| Saber Jelokhani-niaraki1؛ mojtaba Tahmoorespur2؛ Zarrin Minuchehr3؛ Ehsan Motamedian4؛ Mohammad Reza Nassiri2 | ||
| 1Faculty Member of Biotechnology Department-Animal Science Research Institute of Iran | ||
| 2Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran. | ||
| 3Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran. | ||
| 4Department of Biotechnology, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran. | ||
| چکیده [English] | ||
| Streptococcus bovis has been considered to be one of the starch utilizers and lactate producers in the rumen. By considering the role of S. bovis as main lactic acid producer, a large amount of biological information about this strain has been published. But there has not been a systematic analysis of metabolic capabilities for S. bovis so far. In the present study, the first genome-scale metabolic model of S. bovis (iStr472) was reconstructed based on the genome annotation of S. bovis B315. The model was analyzed in terms of sensitivity, topology and capabilities for utilization of other substrates. Results revealed that iStr472 comprises 694 reactions, 626 metabolites and 472 genes. The majority of reactions were located on the nucleotides metabolic pathway. The metabolic genes of model estimated as 27.6 % of all coding genes. Comparison of two models (iStr472 and ModelSEED) indicated that iStr472 has a higher accuracy and validity than the ModelSEED. The 16 highly connected metabolites were found in the model. The results of reaction deletion presented that the model has 126 vital reactions essential for the organism's growth. According to the model prediction, production of biomass was inversely influenced by lactate production. The iStr472 is also capable of utilizing fructose as carbon source. Taken together, it would be possible to use the predictions of iStr472 as a tool for better understanding the metabolism and metabolic engineering of S. bovis for reduced lactate production in the rumen. | ||
| کلیدواژهها [English] | ||
| Streptococcus bovis, genome-scale metabolic model, iStr472, Rumen, COBRA | ||
| مراجع | ||
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