The preliminary essential gene list is based on literature sources. As described in the modeling section of this wiki, the metabolic genes from this preliminary list were used as a starting point for the computer model and were greatly altered based on the model's suggestions. Non-metabolic genes in the this preliminary list were retained in the final list, described in the "Gene Selection" tab.

Criteria for Gene Selection:

• Genes must be present in more than one literature list unless there is particular reason to suspect they are essential.
• The BioBytes metabolism is modeled after the minimal metabolism proposed by Gil et al 04, with the addition of cell wall, fatty acid, heme and ubiquitin synthesis, as Gil assumed these would not be necessary in a mycoplasma like minimal cell.
• Additional genes required for metabolism were selected based on pathway information in the Ecocyc database. Redundancy of pathways is likely why these genes don’t appear essential in Baba, Gerdes and PEC.
• Antitoxin genes are not essential as toxin genes would not be present.

Genes for the following processes were included:

• DNA replication and cell division, but no DNA repair
• Chaperones, but no heat shock or membrane stress response system
• Transcription
• Translation
• Glycolysis
• PMF generation via an ATP synthase consuming ATP to export protons.
• Synthesis of acetyl-CoA from pyruvate
• Fatty acid synthesis
• Methylerithritol pathway (for undecaprenyl phosphate and a ubiquinone side chain)
• Synthesis of phosphatidylethanolamine, but no other phospholipids
• Pentose phosphate pathway (converts 6 or 3 carbon sugars to 5C sugars, such as ones needed in nucleotide biosynthesis)
• Lipoprotein synthesis (Int and lolB are lipoproteins and essential)
• Synthesis of nucleotides (deoxy and oxy) from nucleosides
• Attaching lipid and biotin groups to protein
• Transport:
• PTC transport system (imports and phosphorylates glucose)
• Inorganic phosphate transport
• Nucleoside transport
• Sec system (exports proteins to periplasm), including SRP for cotranslational membrane insertion. secB chaperone does not appear essential. There is NO tat system, which would be used to export cofactor containing folded proteins.
• Lipoprotein transport to outermembrane
• Glutathione transport
• Cofactor synthesis:
• Riboflavin from GTP and ribulose-5-phosphate
• FAD from riboflavin
• NAD from nicotinamide
• NADPH from NAD
• CoA from pantothenic acid
• Methylene tetrahydroxyfolate (mTHF) from folic acid
• S-adenosylmethionine (SAM) from methionine
• Thiamine diphosphate (TPP) from thiamine
• Pyridoxal-5-phosphate (PP) from pyridoxal
• Heme from glutamate
• Ubiquinone

RNAs:

The rrnC operon supplies all the rRNA’s and three of the tRNAs. This operon was selected because it includes the great number of tRNA’s. To select the other tRNA’s, all tRNA’s listed as essential in PEC were first included. One tRNA was then selected for each anticodon that differed on one of the last two bases. Differences in the first base can be accommodated by anticodon 'wobble'. At least one tRNA was included for each amino acid.

The complete list of essential RNA’s can be found here .