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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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The role of horizontal gene transfer in the evolution of sensory systems in PCC 7942. Several proteins containing diguanylate cyclase and other domains involved in signal transduction mechanisms are predicted to be xenologs. Here we show a) a neighbor-joining tree reconstructed using the diguanylate-cyclase domain (86 sites, Poisson correction, 100 bootstrap replicates, branches with bootstraps below 50 are collapsed) from these proteins. Those proteins predicted to be xenologs are colored with red branches in the tree; b) domain structure of proteins following Pfam database [52].
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Figure 12: The role of horizontal gene transfer in the evolution of sensory systems in PCC 7942. Several proteins containing diguanylate cyclase and other domains involved in signal transduction mechanisms are predicted to be xenologs. Here we show a) a neighbor-joining tree reconstructed using the diguanylate-cyclase domain (86 sites, Poisson correction, 100 bootstrap replicates, branches with bootstraps below 50 are collapsed) from these proteins. Those proteins predicted to be xenologs are colored with red branches in the tree; b) domain structure of proteins following Pfam database [52].

Mentions: Among genes belonging to 'Signal transductions mechanisms' category, it was particularly notable that, out of 17 genes having a diguanylate cyclase domain, 11 were predicted to be xenologs (Figure 12). As suggested by domains present in these proteins, they might participate in two component signal transduction systems. For instance GGDEF and EAL domains are involved in the turnover of cyclic-di-GMP in vivo [38]. On the other hand, PAS domains were found to act as sensors for light and oxygen in signal transduction systems [39]. Signal receiver domains [40] and GAF domains involved in regulation of cGMP [41] as well as the integral membrane sensory domain MASE1 [42] were also found. These data suggest that PCC 7942 could have acquired many environmental sensing capabilities through HGT.


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)

The role of horizontal gene transfer in the evolution of sensory systems in PCC 7942. Several proteins containing diguanylate cyclase and other domains involved in signal transduction mechanisms are predicted to be xenologs. Here we show a) a neighbor-joining tree reconstructed using the diguanylate-cyclase domain (86 sites, Poisson correction, 100 bootstrap replicates, branches with bootstraps below 50 are collapsed) from these proteins. Those proteins predicted to be xenologs are colored with red branches in the tree; b) domain structure of proteins following Pfam database [52].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 12: The role of horizontal gene transfer in the evolution of sensory systems in PCC 7942. Several proteins containing diguanylate cyclase and other domains involved in signal transduction mechanisms are predicted to be xenologs. Here we show a) a neighbor-joining tree reconstructed using the diguanylate-cyclase domain (86 sites, Poisson correction, 100 bootstrap replicates, branches with bootstraps below 50 are collapsed) from these proteins. Those proteins predicted to be xenologs are colored with red branches in the tree; b) domain structure of proteins following Pfam database [52].
Mentions: Among genes belonging to 'Signal transductions mechanisms' category, it was particularly notable that, out of 17 genes having a diguanylate cyclase domain, 11 were predicted to be xenologs (Figure 12). As suggested by domains present in these proteins, they might participate in two component signal transduction systems. For instance GGDEF and EAL domains are involved in the turnover of cyclic-di-GMP in vivo [38]. On the other hand, PAS domains were found to act as sensors for light and oxygen in signal transduction systems [39]. Signal receiver domains [40] and GAF domains involved in regulation of cGMP [41] as well as the integral membrane sensory domain MASE1 [42] were also found. These data suggest that PCC 7942 could have acquired many environmental sensing capabilities through HGT.

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