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Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942.

Delaye L, González-Domenech CM, Garcillán-Barcia MP, Peretó J, de la Cruz F, Moya A - BMC Genomics (2011)

Bottom Line: We considered that genes in genomic islands could be found if they showed a combination of: a) unusual G+C content; b) unusual phylogenetic similarity; and/or c) a small number of the highly iterated palindrome 1 (HIP1) motif plus an unusual codon usage.Our estimates of genomic islands in PCC 7942 are larger than those predicted by other published methods like SIGI-HMM.Our results set a guide to non-essential genes in S. elongatus PCC 7942 indicating a path towards the engineering of a model photoautotrophic bacterial cell.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, Spain.

ABSTRACT

Background: Simpler biological systems should be easier to understand and to engineer towards pre-defined goals. One way to achieve biological simplicity is through genome minimization. Here we looked for genomic islands in the fresh water cyanobacteria Synechococcus elongatus PCC 7942 (genome size 2.7 Mb) that could be used as targets for deletion. We also looked for conserved genes that might be essential for cell survival.

Results: By using a combination of methods we identified 170 xenologs, 136 ORFans and 1401 core genes in the genome of S. elongatus PCC 7942. These represent 6.5%, 5.2% and 53.6% of the annotated genes respectively. We considered that genes in genomic islands could be found if they showed a combination of: a) unusual G+C content; b) unusual phylogenetic similarity; and/or c) a small number of the highly iterated palindrome 1 (HIP1) motif plus an unusual codon usage. The origin of the largest genomic island by horizontal gene transfer (HGT) could be corroborated by lack of coverage among metagenomic sequences from a fresh water microbialite. Evidence is also presented that xenologous genes tend to cluster in operons. Interestingly, most genes coding for proteins with a diguanylate cyclase domain are predicted to be xenologs, suggesting a role for horizontal gene transfer in the evolution of Synechococcus sensory systems.

Conclusions: Our estimates of genomic islands in PCC 7942 are larger than those predicted by other published methods like SIGI-HMM. Our results set a guide to non-essential genes in S. elongatus PCC 7942 indicating a path towards the engineering of a model photoautotrophic bacterial cell.

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Distribution of G+C content among ORFs in PCC 7942. Each dot corresponds to an ORF in PCC 7942. The X axis indicated gene size translated into amino acids. Y axis indicated G+C content deviation from the mean. Mean and ± 1SD are shown by gray and doted lines respectively.
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Figure 7: Distribution of G+C content among ORFs in PCC 7942. Each dot corresponds to an ORF in PCC 7942. The X axis indicated gene size translated into amino acids. Y axis indicated G+C content deviation from the mean. Mean and ± 1SD are shown by gray and doted lines respectively.

Mentions: Although G+C deviation by itself is not a precise indicator of xenology, it can be useful in identifying recently acquired genes if it is used in combination with the other lines of evidence. In PCC 7942 there are 174 and 317 genes with a G+C content above, and below 1SD from the average, respectively (Figure 7).


Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942.

Delaye L, González-Domenech CM, Garcillán-Barcia MP, Peretó J, de la Cruz F, Moya A - BMC Genomics (2011)

Distribution of G+C content among ORFs in PCC 7942. Each dot corresponds to an ORF in PCC 7942. The X axis indicated gene size translated into amino acids. Y axis indicated G+C content deviation from the mean. Mean and ± 1SD are shown by gray and doted lines respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3025956&req=5

Figure 7: Distribution of G+C content among ORFs in PCC 7942. Each dot corresponds to an ORF in PCC 7942. The X axis indicated gene size translated into amino acids. Y axis indicated G+C content deviation from the mean. Mean and ± 1SD are shown by gray and doted lines respectively.
Mentions: Although G+C deviation by itself is not a precise indicator of xenology, it can be useful in identifying recently acquired genes if it is used in combination with the other lines of evidence. In PCC 7942 there are 174 and 317 genes with a G+C content above, and below 1SD from the average, respectively (Figure 7).

Bottom Line: We considered that genes in genomic islands could be found if they showed a combination of: a) unusual G+C content; b) unusual phylogenetic similarity; and/or c) a small number of the highly iterated palindrome 1 (HIP1) motif plus an unusual codon usage.Our estimates of genomic islands in PCC 7942 are larger than those predicted by other published methods like SIGI-HMM.Our results set a guide to non-essential genes in S. elongatus PCC 7942 indicating a path towards the engineering of a model photoautotrophic bacterial cell.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, Spain.

ABSTRACT

Background: Simpler biological systems should be easier to understand and to engineer towards pre-defined goals. One way to achieve biological simplicity is through genome minimization. Here we looked for genomic islands in the fresh water cyanobacteria Synechococcus elongatus PCC 7942 (genome size 2.7 Mb) that could be used as targets for deletion. We also looked for conserved genes that might be essential for cell survival.

Results: By using a combination of methods we identified 170 xenologs, 136 ORFans and 1401 core genes in the genome of S. elongatus PCC 7942. These represent 6.5%, 5.2% and 53.6% of the annotated genes respectively. We considered that genes in genomic islands could be found if they showed a combination of: a) unusual G+C content; b) unusual phylogenetic similarity; and/or c) a small number of the highly iterated palindrome 1 (HIP1) motif plus an unusual codon usage. The origin of the largest genomic island by horizontal gene transfer (HGT) could be corroborated by lack of coverage among metagenomic sequences from a fresh water microbialite. Evidence is also presented that xenologous genes tend to cluster in operons. Interestingly, most genes coding for proteins with a diguanylate cyclase domain are predicted to be xenologs, suggesting a role for horizontal gene transfer in the evolution of Synechococcus sensory systems.

Conclusions: Our estimates of genomic islands in PCC 7942 are larger than those predicted by other published methods like SIGI-HMM. Our results set a guide to non-essential genes in S. elongatus PCC 7942 indicating a path towards the engineering of a model photoautotrophic bacterial cell.

Show MeSH
Related in: MedlinePlus