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Amino Acid Biosynthetic Pathways01:29

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Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
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Mitochondrial precursors are partially unfolded or loosely folded polypeptide chains. Newly synthesized precursors are inhibited from spontaneously folding into their native conformation by the cytosolic chaperones, heat shock proteins 70 (Hsp70), and mitochondrial import stimulation factors (MSFs). Precursors bound to MSFs are guided to the TOM70-TOM37 receptors, while precursors bound to Hsp70  chaperones are targetted to TOM20-TOM22 receptor complexes.
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Peroxisomes and mitochondria are two important oxygen-utilizing organelles in eukaryotic cells. Mitochondria carry out cellular respiration—the process that converts energy from food into ATP. Peroxisomes carry out a variety of functions, primarily breaking down different substances, such as fatty acids.
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Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
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Transfer RNA Synthesis

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One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After...
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From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes T&#252;6028
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PrecursorFinder: a customized biosynthetic precursor explorer.

Le Yuan1,2,3, Yu Tian1,3, Shaozhen Ding2

  • 1Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, P. R. China.

Bioinformatics (Oxford, England)
|October 11, 2018
PubMed
Summary
This summary is machine-generated.

PrecursorFinder identifies biosynthetic precursors for novel metabolic pathways. This computational tool aids synthetic biology and metabolic engineering by exploring chemical structures and similarities for efficient pathway development.

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Area of Science:

  • Synthetic biology
  • Metabolic engineering
  • Computational chemistry

Background:

  • Synthetic biology holds potential for producing high-value compounds.
  • Many target molecules lack defined biosynthetic pathways.
  • Identifying biosynthetic precursors is critical for pathway construction.

Purpose of the Study:

  • To present PrecursorFinder, a computational tool for identifying biosynthetic precursors.
  • To facilitate the development of novel metabolic pathways for synthetic biology applications.

Main Methods:

  • PrecursorFinder utilizes chemical structure, similarity, and maximum common substructure (MCS) analysis.
  • The platform incorporates a curated database of over 60,000 potential precursors.
  • Data was extracted from over 500,000 scientific literature sources.

Main Results:

  • PrecursorFinder enables efficient exploration of biosynthetic precursors.
  • The tool supports the design of novel biosynthetic pathways.
  • It accelerates research in synthetic biology and metabolic engineering.

Conclusions:

  • PrecursorFinder is a valuable computational resource for the synthetic biology community.
  • The tool enhances the efficiency of metabolic pathway design and engineering.
  • It addresses the need for computer-assisted precursor identification.