Severity: Warning
Message: file_get_contents(https://...@gmail.com&api_key=61f08fa0b96a73de8c900d749fcb997acc09&a=1): Failed to open stream: HTTP request failed! HTTP/1.1 429 Too Many Requests
Filename: helpers/my_audit_helper.php
Line Number: 176
Backtrace:
File: /var/www/html/application/helpers/my_audit_helper.php
Line: 176
Function: file_get_contents
File: /var/www/html/application/helpers/my_audit_helper.php
Line: 250
Function: simplexml_load_file_from_url
File: /var/www/html/application/helpers/my_audit_helper.php
Line: 3122
Function: getPubMedXML
File: /var/www/html/application/controllers/Detail.php
Line: 575
Function: pubMedSearch_Global
File: /var/www/html/application/controllers/Detail.php
Line: 489
Function: pubMedGetRelatedKeyword
File: /var/www/html/index.php
Line: 316
Function: require_once
Defining the essential gene components for a system to be considered alive is a crucial step toward the synthesis of artificial life. Fifteen years ago, Gil and coworkers proposed the core of a putative minimal bacterial genome, which would provide the capability to achieve metabolic homeostasis, reproduce, and evolve to a bacterium in an ideally controlled environment. They also proposed a simplified metabolic chart capable of providing energy and basic components for a minimal living cell. For this work, we have identified the components of the minimal metabolic network based on the aforementioned studies, associated them to the KEGG database and, by applying the MetaDAG methodology, determined its Metabolic Building Blocks (MBB) and reconstructed its metabolic Directed Acyclic Graph (m-DAG). The reaction graph of this metabolic network consists of 80 compounds and 98 reactions, while its m-DAG has 36 MBBs. Additionally, we identified 12 essential reactions in the m-DAG that are critical for maintaining the connectivity of this network. In a similar manner, we reconstructed the m-DAG of JCVI-syn3.0, which is an artificially designed and manufactured viable cell whose genome arose by minimizing the one from JCVI-syn1.0, and of " Nasuia deltocephalinicola", the bacteria with the smallest natural genome known to date. The comparison of the m-DAGs derived from a theoretical, an artificial, and a natural genome denote slightly different lifestyles, with a consistent core metabolism. The MetaDAG methodology we employ uses homogeneous descriptors and identifiers from the KEGG database, so that comparisons between bacterial strains are not only easy but also suitable for many research fields. The modeling of m-DAGs based on minimal metabolisms can be the first step for the synthesis and manipulation of minimal cells.
Download full-text PDF |
Source |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7824019 | PMC |
http://dx.doi.org/10.3390/biology10010005 | DOI Listing |
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