Limits...
The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms.

Beck C, Knoop H, Axmann IM, Steuer R - BMC Genomics (2012)

Bottom Line: We describe genetic diversity found within cyanobacterial genomes, specifically with respect to metabolic functionality.Our results have direct implications for resource allocation and further sequencing projects.It can be extrapolated that the number of newly identified genes still significantly increases with increasing number of new sequenced genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Theoretical Biology, Humboldt-University of Berlin, Invalidenstr, 43, D-10115 Berlin, Germany.

ABSTRACT

Background: Cyanobacteria are among the most abundant organisms on Earth and represent one of the oldest and most widespread clades known in modern phylogenetics. As the only known prokaryotes capable of oxygenic photosynthesis, cyanobacteria are considered to be a promising resource for renewable fuels and natural products. Our efforts to harness the sun's energy using cyanobacteria would greatly benefit from an increased understanding of the genomic diversity across multiple cyanobacterial strains. In this respect, the advent of novel sequencing techniques and the availability of several cyanobacterial genomes offers new opportunities for understanding microbial diversity and metabolic organization and evolution in diverse environments.

Results: Here, we report a whole genome comparison of multiple phototrophic cyanobacteria. We describe genetic diversity found within cyanobacterial genomes, specifically with respect to metabolic functionality. Our results are based on pair-wise comparison of protein sequences and concomitant construction of clusters of likely ortholog genes. We differentiate between core, shared and unique genes and show that the majority of genes are associated with a single genome. In contrast, genes with metabolic function are strongly overrepresented within the core genome that is common to all considered strains. The analysis of metabolic diversity within core carbon metabolism reveals parts of the metabolic networks that are highly conserved, as well as highly fragmented pathways.

Conclusions: Our results have direct implications for resource allocation and further sequencing projects. It can be extrapolated that the number of newly identified genes still significantly increases with increasing number of new sequenced genomes. Furthermore, genome analysis of multiple phototrophic strains allows us to obtain a detailed picture of metabolic diversity that can serve as a starting point for biotechnological applications and automated metabolic reconstructions.

Show MeSH

Related in: MedlinePlus

Diversity of cyanobacterial metabolism. Shown is a clustered heatmap of the association between the 378 shared EC numbers and the 16 cyanobacterial strains. The clustering of cyanobacterial strains is in good agreement with the results shown in Figure 4. With respect to annotated EC numbers, four broad categories can be distinguished: Category A corresponds to EC numbers predominantely annotated for the three Prochlorococcus strains and Syc7803. Category B corresponds to EC numbers associated with only a small number of strains. Category C covers EC numbers that are associated with almost all strains. Category D corresponds to those EC numbers that are associated with most strains, but are less prevalent in the Prochlorococcus strains and Syc7803. The categories are identified by visiual inspection of the clustered heatmap.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3369817&req=5

Figure 7: Diversity of cyanobacterial metabolism. Shown is a clustered heatmap of the association between the 378 shared EC numbers and the 16 cyanobacterial strains. The clustering of cyanobacterial strains is in good agreement with the results shown in Figure 4. With respect to annotated EC numbers, four broad categories can be distinguished: Category A corresponds to EC numbers predominantely annotated for the three Prochlorococcus strains and Syc7803. Category B corresponds to EC numbers associated with only a small number of strains. Category C covers EC numbers that are associated with almost all strains. Category D corresponds to those EC numbers that are associated with most strains, but are less prevalent in the Prochlorococcus strains and Syc7803. The categories are identified by visiual inspection of the clustered heatmap.

Mentions: A multifaceted picture is obtained, if we look how specific enzymes, and hence metabolic capabilities, are distributed across the 16 cyanobacterial strains. To this end, we first limit the analysis to shared EC numbers. Of the total of 759 distinct EC numbers, assigned across all clusters, a subset of 378 EC numbers is associated with more than one, but less than 16 strains. Figure 7 provides a clustered heatmap of the association between these 378 shared EC numbers and the 16 cyanobacterial strains. EC numbers were clustered using the matlab function clustergram with distance 'hamming'. Overall, we can distinguish between four broad categories: First, shared EC numbers that are predominantely annotated with the Prochlorococcus strains, Pro9215, ProMed4, Pro9211 and Syc7803 (Cluster A in Figure 7). Second, shared EC numbers that are only annotated to a small number of strains (Cluster B in Figure 7). Third, shared EC numbers that are annotated to a large number of strains (Cluster C in Figure 7), and, fourth, shared EC numbers that are annotated to almost all strains, except the three Prochlorococcus strains and Syc7803. We note that Figure 7 again underscores the similarity between the three Prochlorococcus strains and Syc7803 that is already apparent in Figure 4 and Table 2.


The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms.

Beck C, Knoop H, Axmann IM, Steuer R - BMC Genomics (2012)

Diversity of cyanobacterial metabolism. Shown is a clustered heatmap of the association between the 378 shared EC numbers and the 16 cyanobacterial strains. The clustering of cyanobacterial strains is in good agreement with the results shown in Figure 4. With respect to annotated EC numbers, four broad categories can be distinguished: Category A corresponds to EC numbers predominantely annotated for the three Prochlorococcus strains and Syc7803. Category B corresponds to EC numbers associated with only a small number of strains. Category C covers EC numbers that are associated with almost all strains. Category D corresponds to those EC numbers that are associated with most strains, but are less prevalent in the Prochlorococcus strains and Syc7803. The categories are identified by visiual inspection of the clustered heatmap.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3369817&req=5

Figure 7: Diversity of cyanobacterial metabolism. Shown is a clustered heatmap of the association between the 378 shared EC numbers and the 16 cyanobacterial strains. The clustering of cyanobacterial strains is in good agreement with the results shown in Figure 4. With respect to annotated EC numbers, four broad categories can be distinguished: Category A corresponds to EC numbers predominantely annotated for the three Prochlorococcus strains and Syc7803. Category B corresponds to EC numbers associated with only a small number of strains. Category C covers EC numbers that are associated with almost all strains. Category D corresponds to those EC numbers that are associated with most strains, but are less prevalent in the Prochlorococcus strains and Syc7803. The categories are identified by visiual inspection of the clustered heatmap.
Mentions: A multifaceted picture is obtained, if we look how specific enzymes, and hence metabolic capabilities, are distributed across the 16 cyanobacterial strains. To this end, we first limit the analysis to shared EC numbers. Of the total of 759 distinct EC numbers, assigned across all clusters, a subset of 378 EC numbers is associated with more than one, but less than 16 strains. Figure 7 provides a clustered heatmap of the association between these 378 shared EC numbers and the 16 cyanobacterial strains. EC numbers were clustered using the matlab function clustergram with distance 'hamming'. Overall, we can distinguish between four broad categories: First, shared EC numbers that are predominantely annotated with the Prochlorococcus strains, Pro9215, ProMed4, Pro9211 and Syc7803 (Cluster A in Figure 7). Second, shared EC numbers that are only annotated to a small number of strains (Cluster B in Figure 7). Third, shared EC numbers that are annotated to a large number of strains (Cluster C in Figure 7), and, fourth, shared EC numbers that are annotated to almost all strains, except the three Prochlorococcus strains and Syc7803. We note that Figure 7 again underscores the similarity between the three Prochlorococcus strains and Syc7803 that is already apparent in Figure 4 and Table 2.

Bottom Line: We describe genetic diversity found within cyanobacterial genomes, specifically with respect to metabolic functionality.Our results have direct implications for resource allocation and further sequencing projects.It can be extrapolated that the number of newly identified genes still significantly increases with increasing number of new sequenced genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Theoretical Biology, Humboldt-University of Berlin, Invalidenstr, 43, D-10115 Berlin, Germany.

ABSTRACT

Background: Cyanobacteria are among the most abundant organisms on Earth and represent one of the oldest and most widespread clades known in modern phylogenetics. As the only known prokaryotes capable of oxygenic photosynthesis, cyanobacteria are considered to be a promising resource for renewable fuels and natural products. Our efforts to harness the sun's energy using cyanobacteria would greatly benefit from an increased understanding of the genomic diversity across multiple cyanobacterial strains. In this respect, the advent of novel sequencing techniques and the availability of several cyanobacterial genomes offers new opportunities for understanding microbial diversity and metabolic organization and evolution in diverse environments.

Results: Here, we report a whole genome comparison of multiple phototrophic cyanobacteria. We describe genetic diversity found within cyanobacterial genomes, specifically with respect to metabolic functionality. Our results are based on pair-wise comparison of protein sequences and concomitant construction of clusters of likely ortholog genes. We differentiate between core, shared and unique genes and show that the majority of genes are associated with a single genome. In contrast, genes with metabolic function are strongly overrepresented within the core genome that is common to all considered strains. The analysis of metabolic diversity within core carbon metabolism reveals parts of the metabolic networks that are highly conserved, as well as highly fragmented pathways.

Conclusions: Our results have direct implications for resource allocation and further sequencing projects. It can be extrapolated that the number of newly identified genes still significantly increases with increasing number of new sequenced genomes. Furthermore, genome analysis of multiple phototrophic strains allows us to obtain a detailed picture of metabolic diversity that can serve as a starting point for biotechnological applications and automated metabolic reconstructions.

Show MeSH
Related in: MedlinePlus