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A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1.

de Berardinis V, Vallenet D, Castelli V, Besnard M, Pinet A, Cruaud C, Samair S, Lechaplais C, Gyapay G, Richez C, Durot M, Kreimeyer A, Le Fèvre F, Schächter V, Pezo V, Döring V, Scarpelli C, Médigue C, Cohen GN, Marlière P, Salanoubat M, Weissenbach J - Mol. Syst. Biol. (2008)

Bottom Line: A total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium.Several strategies were undertaken to investigate ADP1 metabolism by (1) searching for discrepancies between our essentiality data and current metabolic knowledge, (2) comparing this essentiality data set to those from other organisms, (3) systematic phenotyping of the mutant collection on a variety of carbon sources (quinate, 2-3 butanediol, glucose, etc.).This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches.

View Article: PubMed Central - PubMed

Affiliation: Genoscope, Institut de Génomique (CEA), Evry, France. vberard@genoscope.fr

ABSTRACT
We have constructed a collection of single-gene deletion mutants for all dispensable genes of the soil bacterium Acinetobacter baylyi ADP1. A total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium. This essentiality data set is 88% consistent with the Escherichia coli data set inferred from the Keio mutant collection profiled for growth on minimal medium, while 80% of the orthologous genes described as essential in Pseudomonas aeruginosa are also essential in ADP1. Several strategies were undertaken to investigate ADP1 metabolism by (1) searching for discrepancies between our essentiality data and current metabolic knowledge, (2) comparing this essentiality data set to those from other organisms, (3) systematic phenotyping of the mutant collection on a variety of carbon sources (quinate, 2-3 butanediol, glucose, etc.). This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches.

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Comparison of ADP1, E. coli and P. aeruginosa essentiality data according to TIGR role classification on (A) the medium used to obtain the mutants, (B) on minimal medium. White and blue areas correspond to nonessential and essential genes, respectively. The red area concerns the main categories notably impacted by the medium used for the mutant construction.
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f5: Comparison of ADP1, E. coli and P. aeruginosa essentiality data according to TIGR role classification on (A) the medium used to obtain the mutants, (B) on minimal medium. White and blue areas correspond to nonessential and essential genes, respectively. The red area concerns the main categories notably impacted by the medium used for the mutant construction.

Mentions: ADP1 CDS were classified into different functional roles according to the TIGR classification. The distribution of the essential genes of ADP1, E. coli (Baba et al, 2006) and P. aeruginosa (Liberati et al, 2006) into functional categories is shown in Figure 5A. For three functional categories (biosynthesis of amino acids, cofactors/prosthetic groups and purines/pyrimidines/nucleosides/nucleotides), the percentage of essential genes is significantly higher in ADP1 than in the other species, which could reflect the different media used in the construction of the libraries (minimal versus rich medium). We, therefore, compared our data to an extended set of essential genes that included conditional essential genes (or CEG; mutants growing very poorly (OD<0.1) on minimal medium supplemented with glucose), which was available for E. coli in the Keio collection (EEGS for ‘Extended Essential Gene Set'; see Figure 5B). For two of the three categories of essential genes that appeared significantly lower in E. coli, the comparison with the EEGS resulted in a ratio and a number of essential genes that were very similar to the ones observed in ADP1. For the last category (synthesis of purines, pyrimidines, nucleosides and nucleotides), although the number of essential genes is similar, the percentage difference is only reduced, mainly because a higher number of genes were assigned to this category in E. coli (80 versus 44 in ADP1). For example, the salvage pathway of nucleosides and nucleotides, which does not exist in ADP1, involves at least 20 genes in E. coli. The other functional categories are not notably influenced by the medium used for the mutant construction.


A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1.

de Berardinis V, Vallenet D, Castelli V, Besnard M, Pinet A, Cruaud C, Samair S, Lechaplais C, Gyapay G, Richez C, Durot M, Kreimeyer A, Le Fèvre F, Schächter V, Pezo V, Döring V, Scarpelli C, Médigue C, Cohen GN, Marlière P, Salanoubat M, Weissenbach J - Mol. Syst. Biol. (2008)

Comparison of ADP1, E. coli and P. aeruginosa essentiality data according to TIGR role classification on (A) the medium used to obtain the mutants, (B) on minimal medium. White and blue areas correspond to nonessential and essential genes, respectively. The red area concerns the main categories notably impacted by the medium used for the mutant construction.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2290942&req=5

f5: Comparison of ADP1, E. coli and P. aeruginosa essentiality data according to TIGR role classification on (A) the medium used to obtain the mutants, (B) on minimal medium. White and blue areas correspond to nonessential and essential genes, respectively. The red area concerns the main categories notably impacted by the medium used for the mutant construction.
Mentions: ADP1 CDS were classified into different functional roles according to the TIGR classification. The distribution of the essential genes of ADP1, E. coli (Baba et al, 2006) and P. aeruginosa (Liberati et al, 2006) into functional categories is shown in Figure 5A. For three functional categories (biosynthesis of amino acids, cofactors/prosthetic groups and purines/pyrimidines/nucleosides/nucleotides), the percentage of essential genes is significantly higher in ADP1 than in the other species, which could reflect the different media used in the construction of the libraries (minimal versus rich medium). We, therefore, compared our data to an extended set of essential genes that included conditional essential genes (or CEG; mutants growing very poorly (OD<0.1) on minimal medium supplemented with glucose), which was available for E. coli in the Keio collection (EEGS for ‘Extended Essential Gene Set'; see Figure 5B). For two of the three categories of essential genes that appeared significantly lower in E. coli, the comparison with the EEGS resulted in a ratio and a number of essential genes that were very similar to the ones observed in ADP1. For the last category (synthesis of purines, pyrimidines, nucleosides and nucleotides), although the number of essential genes is similar, the percentage difference is only reduced, mainly because a higher number of genes were assigned to this category in E. coli (80 versus 44 in ADP1). For example, the salvage pathway of nucleosides and nucleotides, which does not exist in ADP1, involves at least 20 genes in E. coli. The other functional categories are not notably influenced by the medium used for the mutant construction.

Bottom Line: A total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium.Several strategies were undertaken to investigate ADP1 metabolism by (1) searching for discrepancies between our essentiality data and current metabolic knowledge, (2) comparing this essentiality data set to those from other organisms, (3) systematic phenotyping of the mutant collection on a variety of carbon sources (quinate, 2-3 butanediol, glucose, etc.).This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches.

View Article: PubMed Central - PubMed

Affiliation: Genoscope, Institut de Génomique (CEA), Evry, France. vberard@genoscope.fr

ABSTRACT
We have constructed a collection of single-gene deletion mutants for all dispensable genes of the soil bacterium Acinetobacter baylyi ADP1. A total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium. This essentiality data set is 88% consistent with the Escherichia coli data set inferred from the Keio mutant collection profiled for growth on minimal medium, while 80% of the orthologous genes described as essential in Pseudomonas aeruginosa are also essential in ADP1. Several strategies were undertaken to investigate ADP1 metabolism by (1) searching for discrepancies between our essentiality data and current metabolic knowledge, (2) comparing this essentiality data set to those from other organisms, (3) systematic phenotyping of the mutant collection on a variety of carbon sources (quinate, 2-3 butanediol, glucose, etc.). This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches.

Show MeSH
Related in: MedlinePlus