Determination of the core of a minimal bacterial gene set

Abstract

The availability of a large number of complete genome sequences raises the question of how many genes are essential for cellular life. Trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. Six of the analyzed genomes are very small due to a dramatic genome size reduction process, while the other two, corresponding to free-living relatives, are larger. The available data from several systematic experimental approaches to define all the essential genes in some completely sequenced bacterial genomes were also considered, and a reconstruction of a minimal metabolic machinery necessary to sustain life was carried out. The proposed minimal genome contains 206 protein-coding genes with all the genetic information necessary for self-maintenance and reproduction in the presence of a full complement of essential nutrients and in the absence of environmental stress. The main features of such a minimal gene set, as well as the metabolic functions that must be present in the hypothetical minimal cell, are discussed.

FIG. 1.

A minimal metabolism. The minimal cell can obtain its more basic components from the environment: glucose, fatty acids, amino acids, adenine, guanine, uracil, and coenzyme precursors (nicotinamide, riboflavin, folate, pantothenate, and pyridoxal). Each box includes the metabolic transformations classified in major groups of pathways: glycolysis, phospholipid biosynthesis, nonoxidative pentose-phosphate pathway, nucleotide biosynthesis, synthesis of enzymatic cofactors, and synthesis of protein precursors, i.e., aminoacyl-tRNAs (aa-tRNA). Arrows with discontinuous lines represent incorporation from the environment. Single continuous arrows represent single enzymatic steps, whereas wide arrows represent several enzymatic steps (the number within the arrow indicates the number of steps). Lines with a final black point indicate the necessity of metabolites for some of the transformations inside the corresponding box. Metabolic intermediates and final pathway products are in green boxes. Metabolites acting as a source of chemical energy are in red boxes. Reducing-power cofactors are in light blue boxes. Abbreviations (besides the accepted symbols and those defined in the text): PEP, phosphoenolpyruvate; G6P, glucose-6-phosphate; Gd3P, glyceraldehyde-3-phosphate; DHAP, dihydroxyacetonephosphate; G3P, sn-glycerol-3-phosphate; CDP-DAG, CDP-diacylglycerol; SAM, S-adenosylmethionine; THF, tetrahydrofolate. Metabolic precursors of external origin are in gray boxes.

FIG. 2.

A minimal nucleotide metabolism based on salvage pathways. Activated ribonucleotides and deoxyribonucleotides are obtained from free bases (A, G, and U), PRPP, ATP-dependent phosphorylating reactions, and NADH-dependent reduction. White boxes indicate the individual enzymatic activity (EC number and coding gene). Other colors are used as in Fig. 1.

FIG. 3.

Biosynthesis of cofactors. A metabolism of essential cofactors used by the minimal cell starting with precursors (i.e., vitamins): nicotinamide, riboflavin, thiamine, pyridoxal, patothenic acid, methionine, and folic acid. Yellow boxes indicate the enzymes that need each cofactor for their correct function. Other colors and symbols are as in Fig. 1 and 2. PP, pyridoxal-phosphate.