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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.

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Comparison of CLOGs with and without assigned EC numbers. A - A bar plot of the number of CLOGs with and without assigned EC number in all 16 strains. B - Number of CLOGs with assigned EC number compared to CLOGs without assigned EC number in the strains of different size. The red line indicates a least square regression line to highlight the tendency of the data. The data shows a weak correlation of size (total number of CLOGs) and number of CLOGs with assigned EC numbers.
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Figure 6: Comparison of CLOGs with and without assigned EC numbers. A - A bar plot of the number of CLOGs with and without assigned EC number in all 16 strains. B - Number of CLOGs with assigned EC number compared to CLOGs without assigned EC number in the strains of different size. The red line indicates a least square regression line to highlight the tendency of the data. The data shows a weak correlation of size (total number of CLOGs) and number of CLOGs with assigned EC numbers.

Mentions: Using the set of CLOGs described above, 1851 CLOGs of the 21238 can be regarded as metabolic. We note that due to bifunctional enzymes or inconsistent and erroneous annotation CLOGs may be assigned to more than one metabolic function. However, in our case only 66 CLOGs (out of 1851) are assigned to more than one EC number, with a total of 759 distinct EC numbers assigned across all clusters. These results indicate that inconsistent annotation does not significantly constrain our analysis, even without prior filtering or manual curation. Figure 5 shows the distribution of metabolic CLOGs across the unique, shared and core genome. CLOGs assigned to metabolic function are highly overrepresented within the set that is common to all 16 cyanobacterial strains, with about 55% of all core CLOGs associated with metabolic function. Obviously, cellular metabolism, defined here as genes assigned to enzymatic function, constitutes a large fraction of the core genome. Figure 6 gives the percentage of CLOGs assigned to enzymatic function across all 16 strains considered in this study. The number of enzymatic CLOGs increases linearly with the number of total CLOGs assigned to each strain, with an offset of about 500 core enzymatic CLOGs. However, the correlation between number of enzymatic and total CLOGs is rather weak and dominated by the contribution from enzymatic core CLOGs. A further analysis of the respective pathways and enzyme classes associated to CLOGs revealed no obvious difference between unique and core genes, that is, no particular enzymatic category or pathway was strongly overrepresented in either class. Nonetheless, a number of core pathways can be identified that are common to all 16 cyanobacterial strains. Among the highly conserved pathways are the Calvin Benson cycle, the oxidative pentose phosphate pathway, nucleotide synthesis, and amino acids synthesis. However, with respect to the latter, a number of phosphatases and transaminases are not annotated in several strains.


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

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

Comparison of CLOGs with and without assigned EC numbers. A - A bar plot of the number of CLOGs with and without assigned EC number in all 16 strains. B - Number of CLOGs with assigned EC number compared to CLOGs without assigned EC number in the strains of different size. The red line indicates a least square regression line to highlight the tendency of the data. The data shows a weak correlation of size (total number of CLOGs) and number of CLOGs with assigned EC numbers.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Comparison of CLOGs with and without assigned EC numbers. A - A bar plot of the number of CLOGs with and without assigned EC number in all 16 strains. B - Number of CLOGs with assigned EC number compared to CLOGs without assigned EC number in the strains of different size. The red line indicates a least square regression line to highlight the tendency of the data. The data shows a weak correlation of size (total number of CLOGs) and number of CLOGs with assigned EC numbers.
Mentions: Using the set of CLOGs described above, 1851 CLOGs of the 21238 can be regarded as metabolic. We note that due to bifunctional enzymes or inconsistent and erroneous annotation CLOGs may be assigned to more than one metabolic function. However, in our case only 66 CLOGs (out of 1851) are assigned to more than one EC number, with a total of 759 distinct EC numbers assigned across all clusters. These results indicate that inconsistent annotation does not significantly constrain our analysis, even without prior filtering or manual curation. Figure 5 shows the distribution of metabolic CLOGs across the unique, shared and core genome. CLOGs assigned to metabolic function are highly overrepresented within the set that is common to all 16 cyanobacterial strains, with about 55% of all core CLOGs associated with metabolic function. Obviously, cellular metabolism, defined here as genes assigned to enzymatic function, constitutes a large fraction of the core genome. Figure 6 gives the percentage of CLOGs assigned to enzymatic function across all 16 strains considered in this study. The number of enzymatic CLOGs increases linearly with the number of total CLOGs assigned to each strain, with an offset of about 500 core enzymatic CLOGs. However, the correlation between number of enzymatic and total CLOGs is rather weak and dominated by the contribution from enzymatic core CLOGs. A further analysis of the respective pathways and enzyme classes associated to CLOGs revealed no obvious difference between unique and core genes, that is, no particular enzymatic category or pathway was strongly overrepresented in either class. Nonetheless, a number of core pathways can be identified that are common to all 16 cyanobacterial strains. Among the highly conserved pathways are the Calvin Benson cycle, the oxidative pentose phosphate pathway, nucleotide synthesis, and amino acids synthesis. However, with respect to the latter, a number of phosphatases and transaminases are not annotated in several strains.

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