scholarly journals Enumerating all possible biosynthetic pathways from metabolic networks

2017 ◽  
Author(s):  
Aarthi Ravikrishnan ◽  
Meghana Nasre ◽  
Karthik Raman
Keyword(s):  
Microbial Communities ◽  
Metabolic Networks ◽  
Amino Acid Biosynthesis ◽  
Breadth First Search ◽  
Acid Biosynthesis ◽  
Complex Molecules ◽  
Graph Theoretic ◽  
Metabolic Interactions ◽  
Target Molecules ◽  
Precursor Molecules

AbstractExhaustive identification of all alternate possible pathways that exist within metabolic networks can provide valuable insights into cellular metabolism. With the growing number of metabolic reconstructions, there is a need for an efficient method to enumerate pathways, which can also scale well to large metabolic networks, such as those corresponding to microbial communities.We developed MetQuest, an efficient graph-theoretic algorithm to enumerate all possible pathways of a particular length between a given set of source and target molecules. Our algorithm employs aguidedbreadth-first search to identify all feasible reactions based on the availability of the precursor molecules, followed by a novel dynamic-programming based enumeration, which assembles these reactions into pathways producing the target from the source. We demonstrate several interesting applications of our algorithm, ranging from predicting amino acid biosynthesis pathways to identifying the most diverse pathways involved in degradation of complex molecules. We also illustrate the scalability of our algorithm, by studying larger graphs such as those corresponding to microbial communities, and identify several metabolic interactions happening therein.A Python-based implementation of MetQuest is available athttps://github.com/RamanLab/MetQuest

scholarly journals Quantifying biosynthetic network robustness across the human oral microbiome

2018 ◽  
Author(s):  
David B. Bernstein ◽  
Floyd E. Dewhirst ◽  
Daniel Segrè
Keyword(s):  
Microbial Communities ◽  
Metabolic Networks ◽  
Oral Microbiome ◽  
Network Robustness ◽  
Species Comparison ◽  
Metabolic Products ◽  
Metabolic Interactions

AbstractMetabolic interactions, such as cross-feeding, play a prominent role in microbial communitystructure. For example, they may underlie the ubiquity of uncultivated microorganisms. We investigated this phenomenon in the human oral microbiome, by analyzing microbial metabolic networks derived from sequenced genomes. Specifically, we devised a probabilistic biosynthetic network robustness metric that describes the chance that an organism could produce a given metabolite, and used it to assemble a comprehensive atlas of biosynthetic capabilities for 88 metabolites across 456 human oral microbiome strains. A cluster of organisms characterized by reduced biosynthetic capabilities stood out within this atlas. This cluster included several uncultivated taxa and three recently co-culturedSaccharibacteria(TM7) phylum species. Comparison across strains also allowed us to systematically identify specific putative metabolic interdependences between organisms. Our method, which provides a new way of converting annotated genomes into metabolic predictions, is easily extendible to other microbial communities and metabolic products.

Structure of the yeast HIS5 gene responsive to general control of amino acid biosynthesis

1987 ◽  
Vol 208 (1-2) ◽  
pp. 159-167 ◽  
Author(s):  
Kiyoji Nishiwaki ◽  
Naoyuki Hayashi ◽  
Shinji Irie ◽  
Dong-Hyo Chung ◽  
Satoshi Harashima ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Biosynthesis ◽  
General Control ◽  
Acid Biosynthesis

scholarly journals Incorporation of alternative amino acids into cyanophycin by different cyanophycin synthetases heterologously expressed in Corynebacterium glutamicum

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ramona Wördemann ◽  
Lars Wiefel ◽  
Volker F. Wendisch ◽  
Alexander Steinbüchel
Keyword(s):  
Amino Acids ◽  
Dry Weight ◽  
Growth Conditions ◽  
Amino Acid Biosynthesis ◽  
Water Soluble ◽  
Lysine Content ◽  
Polyaspartic Acid ◽  
Acid Biosynthesis ◽  
Cyanophycin Synthetase ◽  
Potential Precursor

AbstractCyanophycin (multi-l-arginyl-poly-l-aspartic acid; also known as cyanophycin grana peptide [CGP]) is a biopolymer that could be used in various fields, for example, as a potential precursor for the synthesis of polyaspartic acid or for the production of CGP-derived dipeptides. To extend the applications of this polymer, it is therefore of interest to synthesize CGP with different compositions. A recent re-evaluation of the CGP synthesis in C. glutamicum has shown that C. glutamicum is a potentially interesting microorganism for CGP synthesis with a high content of alternative amino acids. This study shows that the amount of alternative amino acids can be increased by using mutants of C. glutamicum with altered amino acid biosynthesis. With the DM1729 mutant, the lysine content in the polymer could be increased up to 33.5 mol%. Furthermore, an ornithine content of up to 12.6 mol% was achieved with ORN2(Pgdh4). How much water-soluble or insoluble CGP is synthesized is strongly related to the used cyanophycin synthetase. CphADh synthesizes soluble CGP exclusively. However, soluble CGP could also be isolated from cells expressing CphA6308Δ1 or CphA6308Δ1_C595S in addition to insoluble CGP in all examined strains. The point mutation in CphA6308Δ1_C595S partially resulted in a higher lysine content. In addition, the CGP content could be increased to 36% of the cell dry weight under optimizing growth conditions in C. glutamicum ATCC13032. All known alternative major amino acids for CGP synthesis (lysine, ornithine, citrulline, and glutamic acid) could be incorporated into CGP in C. glutamicum.

scholarly journals Transfer RNA-dependent amino acid biosynthesis: An essential route to asparagine formation

2002 ◽  
Vol 99 (5) ◽  
pp. 2678-2683 ◽  
Author(s):  
B. Min ◽  
J. T. Pelaschier ◽  
D. E. Graham ◽  
D. Tumbula-Hansen ◽  
D. Soll
Keyword(s):  
Amino Acid ◽  
Amino Acid Biosynthesis ◽  
Transfer Rna ◽  
Acid Biosynthesis
Sign in / Sign up

Export Citation Format

Share Document