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Amino Acid Biosynthetic Pathways01:29

Amino Acid Biosynthetic Pathways

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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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Nucleic acid biosynthesis is a fundamental biochemical process that produces the purine and pyrimidine nucleotides essential for DNA and RNA synthesis. This pathway maintains a balanced nucleotide pool, preventing imbalances that could jeopardize genetic integrity and cellular function. Given the crucial role of nucleotides, their synthesis is tightly regulated to ensure proper cellular homeostasis.Purine BiosynthesisThe biosynthesis of purine nucleotides begins with ribose-5-phosphate, a...
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Inorganic Nitrogen Assimilation01:22

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Nitrogen is an essential element in biological systems, forming a crucial component of proteins, nucleic acids, and other cellular constituents. Many bacteria and archaea acquire nitrogen in the form of nitrate (NO₃⁻) or ammonia (NH₃), which are then assimilated into biomolecules through specific enzymatic pathways.Assimilatory Nitrate ReductionWhen nitrate enters the cell, it undergoes a two-step reduction process known as assimilatory nitrate reduction. Initially, the enzyme...
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Other Glycolytic Pathways01:24

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The pentose phosphate pathway (PPP) operates in parallel with glycolysis, facilitating the metabolism of both pentoses and glucose. This pathway consists of two distinct phases: the oxidative and non-oxidative phases. While it does not directly generate ATP, the intermediates formed during the process can integrate into glycolysis, contributing to cellular energy metabolism when required.Oxidative Phase: NADPH ProductionThe oxidative phase of the pentose phosphate pathway is primarily...
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Amino Acid Catabolism01:18

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Microorganisms rely on proteins as an essential carbon and energy source, particularly in environments with limited polysaccharides or lipids. However, proteins are too large to cross the plasma membrane unaided, necessitating enzymatic degradation. Microbes secrete extracellular proteases and peptidases that hydrolyze proteins into peptides, which can then be transported across the membrane. Once inside the cell, intracellular proteases degrade these peptides into free amino acids, which...
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Overview of Metabolism01:40

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Living cells constantly carry out various chemical reactions which are necessary for their proper functioning. These reactions are interlinked to one another via multiple pathways. The collection of these chemical reactions is known as metabolism.
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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
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Functional polyamine metabolic enzymes and pathways encoded by the virosphere.

Bin Li1, Jue Liang1, Hamid R Baniasadi1

  • 1Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75214.

Proceedings of the National Academy of Sciences of the United States of America
|February 21, 2023
PubMed
Summary

Viruses utilize host cell machinery, including polyamine metabolism, for replication. This study identifies diverse viral enzymes and pathways involved in spermidine and homospermidine metabolism, revealing their global role in virus biology.

Keywords:
bacteriophagepolyamineputrescinespermidinevirus

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Assaying for Inorganic Polyphosphate in Bacteria
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Area of Science:

  • Virology
  • Molecular Biology
  • Biochemistry

Background:

  • Viruses hijack host cell metabolism and replication systems to produce progeny.
  • Viral genomes often encode metabolic enzymes, acquired from hosts, to manipulate cellular processes.
  • The polyamine spermidine is essential for the replication of both bacteriophages and eukaryotic viruses.

Purpose of the Study:

  • To identify and functionally characterize viral-encoded polyamine metabolic enzymes and pathways.
  • To investigate the role of these viral enzymes in subverting host metabolism for viral replication.
  • To consolidate and expand evidence for the global importance of spermidine in virus biology.

Main Methods:

  • Bioinformatic analysis to identify viral-encoded polyamine metabolic enzymes and pathways.
  • Functional characterization of identified enzymes, including ornithine decarboxylase (ODC), arginine decarboxylase (ADC), arginase, S-adenosylmethionine decarboxylase (AdoMetDC/speD), spermidine synthase, homospermidine synthase, spermidine N-acetyltransferase, and N-acetylspermidine amidohydrolase.
  • Identification of homologs of the spermidine-modified translation factor eIF5a in giant viruses.

Main Results:

  • Diverse viral enzymes and pathways for spermidine and homospermidine metabolism were identified, including pyridoxal 5'-phosphate (PLP)-dependent ODC, pyruvoyl-dependent ODC and ADC, arginase, AdoMetDC/speD, spermidine synthase, homospermidine synthase, spermidine N-acetyltransferase, and N-acetylspermidine amidohydrolase.
  • Some marine phages have evolved AdoMetDC/speD homologs into pyruvoyl-dependent ADC or ODC, and pelagiphages infecting Candidatus Pelagibacter ubique encode both PLP- and pyruvoyl-dependent ADCs.
  • Giant viruses encode complete or partial spermidine/homospermidine biosynthetic pathways, and some can release spermidine or sequester it into an inactive N-acetyl form.

Conclusions:

  • Viral-encoded enzymes and pathways for spermidine and homospermidine metabolism are widespread and diverse.
  • These viral systems play a significant role in manipulating polyamine levels for viral replication.
  • The findings underscore a crucial and global role of spermidine in the biology of various viruses.