Table of contents

Carbon

What it depends on, and why

• Energy: ATP and reducing equivalents support energy-requiring carbon assimilation and precursor production. The exact coupling depends on the chosen fixation pathway.
• Cofactors: CoA and one-carbon cofactors enable carbon transfer and acetyl-CoA metabolism in the proposed network.
• Metal loading: CODH/ACS and other selected carbon-metabolism enzymes require correctly assembled metal centers.

What it supplies, and why

• Cofactors: Carbon intermediates supply the molecular skeletons used to synthesize cofactors.
• Nucleotides: Carbon precursors supply the ribose and ring-building substrates needed for nucleotide synthesis.
• Amino acids: Central metabolism provides carbon skeletons for amino acid biosynthesis.
• Membrane: Acetyl-CoA and other carbon intermediates feed fatty acid and membrane lipid synthesis.

Amino acids

What it depends on, and why

• Carbon: Central metabolism provides carbon skeletons for amino acid biosynthesis.
• Cofactors: Cofactors support amino-group transfer, reduction, and other amino acid biosynthetic reactions.
• Energy: ATP and reducing power drive energy-requiring amino acid biosynthesis.
• Transport: Uptake supplies nitrogen, sulfur, or other environmental substrates needed by the selected biosynthetic routes.

What it supplies, and why

• Cofactors: Amino-acid-derived precursors contribute to pathways such as SAM and other cofactor biosynthesis.
• Nucleotides: Amino acids donate nitrogen and other atoms to purine and pyrimidine biosynthesis.
• RNA: Amino acids are the building blocks loaded onto tRNAs and joined into proteins.
• Metal loading: Cysteine supplies sulfur to selected Fe–S cluster assembly systems.

Nucleotides

What it depends on, and why

• Carbon: Carbon precursors supply the ribose and ring-building substrates needed for nucleotide synthesis.
• Amino acids: Amino acids donate nitrogen and other atoms to purine and pyrimidine biosynthesis.
• Cofactors: Selected nucleotide reactions require one-carbon or redox cofactors.
• Energy: Energy investment supports nucleotide synthesis and phosphorylation.

What it supplies, and why

• Genome: Deoxyribonucleotides are the monomers used to replicate and repair DNA.
• RNA: Ribonucleotides supply RNA synthesis; ATP and GTP also serve as substrates in translation-related reactions.

Cofactors

What it depends on, and why

• Carbon: Carbon intermediates supply the molecular skeletons used to synthesize cofactors.
• Amino acids: Amino-acid-derived precursors contribute to pathways such as SAM and other cofactor biosynthesis.
• Energy: ATP and reducing power drive cofactor synthesis and regeneration.

What it supplies, and why

• Carbon: CoA and one-carbon cofactors enable carbon transfer and acetyl-CoA metabolism in the proposed network.
• Energy: Flavin, NAD, and other cofactors participate in electron-transfer reactions.
• Nucleotides: Selected nucleotide reactions require one-carbon or redox cofactors.
• Amino acids: Cofactors support amino-group transfer, reduction, and other amino acid biosynthetic reactions.
• Membrane: CoA, biotin in selected pathways, and redox cofactors support lipid biosynthesis.

Energy

What it depends on, and why

• Cofactors: Flavin, NAD, and other cofactors participate in electron-transfer reactions.
• Membrane: A sufficiently ion-tight membrane supports electrochemical gradients and houses respiratory and ATP-synthase complexes.
• Metal loading: Selected electron-transfer proteins require Fe–S clusters or other metal centers to function.

What it supplies, and why

• Carbon: ATP and reducing equivalents support energy-requiring carbon assimilation and precursor production. The exact coupling depends on the chosen fixation pathway.
• Cofactors: ATP and reducing power drive cofactor synthesis and regeneration.
• Nucleotides: Energy investment supports nucleotide synthesis and phosphorylation.
• Amino acids: ATP and reducing power drive energy-requiring amino acid biosynthesis.
• Membrane: ATP and reducing power support membrane-component synthesis.
• Genome: ATP powers selected helicase, ligase, and chromosome-management reactions.
• RNA: ATP supports tRNA charging and GTP supports major translation steps; energy supply must replenish these currencies.
• Gene regulation: ATP supports phosphorylation and other energy-dependent regulatory processes.
• Transport: ATP or ion gradients drive active transport, depending on transporter type.
• Internal balance: Energy supply supports pumps and other active maintenance processes.
• Stress: Energy supply supports many protective, repair, and protein-turnover responses.

Membrane

What it depends on, and why

• Carbon: Acetyl-CoA and other carbon intermediates feed fatty acid and membrane lipid synthesis.
• Cofactors: CoA, biotin in selected pathways, and redox cofactors support lipid biosynthesis.
• Energy: ATP and reducing power support membrane-component synthesis.

What it supplies, and why

• Energy: A sufficiently ion-tight membrane supports electrochemical gradients and houses respiratory and ATP-synthase complexes.
• Transport: A membrane provides the physical environment in which transport channels and carriers operate.
• Division: Daughter-cell formation requires expansion and partitioning of the cell envelope.
• Internal balance: Selective membrane permeability allows internal conditions to differ from the surroundings.

Genome

What it depends on, and why

• Nucleotides: Deoxyribonucleotides are the monomers used to replicate and repair DNA.
• Energy: ATP powers selected helicase, ligase, and chromosome-management reactions.
• RNA: Translation produces the proteins that carry out DNA replication, repair, and segregation.

What it supplies, and why

• RNA: Maintained DNA provides templates encoding mRNAs, functional RNAs, and the translation machinery.
• Division: Chromosome replication and segregation must be coordinated with cellular partitioning.

RNA

What it depends on, and why

• Genome: Maintained DNA provides templates encoding mRNAs, functional RNAs, and the translation machinery.
• Nucleotides: Ribonucleotides supply RNA synthesis; ATP and GTP also serve as substrates in translation-related reactions.
• Amino acids: Amino acids are the building blocks loaded onto tRNAs and joined into proteins.
• Energy: ATP supports tRNA charging and GTP supports major translation steps; energy supply must replenish these currencies.
• Internal balance: Compatible pH, ionic strength, and redox conditions support RNA and protein function.

What it supplies, and why

• Genome: Translation produces the proteins that carry out DNA replication, repair, and segregation.
• Gene regulation: Regulators, sensors, kinases, and phosphatases are protein products of translation.
• Transport: Translation supplies channels, pumps, and other transport proteins.
• Division: Translation provides structural and division proteins.
• Stress: Translation replaces damaged proteins and produces stress-response factors.
• Metal loading: Translation supplies scaffolds, sulfur-mobilization enzymes, and maturation factors.

Proteins

What it depends on, and why

• Genome: Maintained DNA provides templates encoding mRNAs, functional RNAs, and the translation machinery.
• Nucleotides: Ribonucleotides supply RNA synthesis; ATP and GTP also serve as substrates in translation-related reactions.
• Amino acids: Amino acids are the building blocks loaded onto tRNAs and joined into proteins.
• Energy: ATP supports tRNA charging and GTP supports major translation steps; energy supply must replenish these currencies.
• Internal balance: Compatible pH, ionic strength, and redox conditions support RNA and protein function.

What it supplies, and why

• Genome: Translation produces the proteins that carry out DNA replication, repair, and segregation.
• Gene regulation: Regulators, sensors, kinases, and phosphatases are protein products of translation.
• Transport: Translation supplies channels, pumps, and other transport proteins.
• Division: Translation provides structural and division proteins.
• Stress: Translation replaces damaged proteins and produces stress-response factors.
• Metal loading: Translation supplies scaffolds, sulfur-mobilization enzymes, and maturation factors.

Division

What it depends on, and why

• Membrane: Daughter-cell formation requires expansion and partitioning of the cell envelope.
• Genome: Chromosome replication and segregation must be coordinated with cellular partitioning.
• RNA: Translation provides structural and division proteins.

What it supplies, and why

none listed

Transport

What it depends on, and why

• Membrane: A membrane provides the physical environment in which transport channels and carriers operate.
• Energy: ATP or ion gradients drive active transport, depending on transporter type.
• RNA: Translation supplies channels, pumps, and other transport proteins.

What it supplies, and why

• Amino acids: Uptake supplies nitrogen, sulfur, or other environmental substrates needed by the selected biosynthetic routes.
• Gene regulation: Uptake and transport determine intracellular nutrient and ion availability, providing inputs to selected regulatory responses.
• Internal balance: Ion transport and solute exchange maintain intracellular pH, osmolarity, and nutrient balance.

Internal balance

What it depends on, and why

• Transport: Ion transport and solute exchange maintain intracellular pH, osmolarity, and nutrient balance.
• Membrane: Selective membrane permeability allows internal conditions to differ from the surroundings.
• Energy: Energy supply supports pumps and other active maintenance processes.

What it supplies, and why

• RNA: Compatible pH, ionic strength, and redox conditions support RNA and protein function.

Stress

What it depends on, and why

• Energy: Energy supply supports many protective, repair, and protein-turnover responses.
• RNA: Translation replaces damaged proteins and produces stress-response factors.

What it supplies, and why

none listed

Metal loading

What it depends on, and why

• Amino acids: Cysteine supplies sulfur to selected Fe–S cluster assembly systems.
• RNA: Translation supplies scaffolds, sulfur-mobilization enzymes, and maturation factors.

What it supplies, and why

• Carbon: CODH/ACS and other selected carbon-metabolism enzymes require correctly assembled metal centers.
• Energy: Selected electron-transfer proteins require Fe–S clusters or other metal centers to function.

Gene regulation

What it depends on, and why

• RNA: Regulators, sensors, kinases, and phosphatases are protein products of translation.
• Energy: ATP supports phosphorylation and other energy-dependent regulatory processes.
• Transport: Uptake and transport determine intracellular nutrient and ion availability, providing inputs to selected regulatory responses.

What it supplies, and why

none listed

Unknown function

What it depends on, and why

none listed

What it supplies, and why

none listed