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Signature proteins for the major clades of Cyanobacteria.

Gupta RS, Mathews DW - BMC Evol. Biol. (2010)

Bottom Line: We also describe 3 conserved indels in flavoprotein, heme oxygenase and protochlorophyllide oxidoreductase proteins that are specific for either Clade C cyanobacteria or for various subclades of Prochlorococcus.These signature proteins and indels provide novel means for circumscription of various cyanobacterial clades in clear molecular terms.Their functional studies should lead to discovery of novel properties that are unique to these groups of cyanobacteria.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada. gupta@mcmaster.ca

ABSTRACT

Background: The phylogeny and taxonomy of cyanobacteria is currently poorly understood due to paucity of reliable markers for identification and circumscription of its major clades.

Results: A combination of phylogenomic and protein signature based approaches was used to characterize the major clades of cyanobacteria. Phylogenetic trees were constructed for 44 cyanobacteria based on 44 conserved proteins. In parallel, Blastp searches were carried out on each ORF in the genomes of Synechococcus WH8102, Synechocystis PCC6803, Nostoc PCC7120, Synechococcus JA-3-3Ab, Prochlorococcus MIT9215 and Prochlor. marinus subsp. marinus CCMP1375 to identify proteins that are specific for various main clades of cyanobacteria. These studies have identified 39 proteins that are specific for all (or most) cyanobacteria and large numbers of proteins for other cyanobacterial clades. The identified signature proteins include: (i) 14 proteins for a deep branching clade (Clade A) of Gloebacter violaceus and two diazotrophic Synechococcus strains (JA-3-3Ab and JA2-3-B'a); (ii) 5 proteins that are present in all other cyanobacteria except those from Clade A; (iii) 60 proteins that are specific for a clade (Clade C) consisting of various marine unicellular cyanobacteria (viz. Synechococcus and Prochlorococcus); (iv) 14 and 19 signature proteins that are specific for the Clade C Synechococcus and Prochlorococcus strains, respectively; (v) 67 proteins that are specific for the Low B/A ecotype Prochlorococcus strains, containing lower ratio of chl b/a2 and adapted to growth at high light intensities; (vi) 65 and 8 proteins that are specific for the Nostocales and Chroococcales orders, respectively; and (vii) 22 and 9 proteins that are uniquely shared by various Nostocales and Oscillatoriales orders, or by these two orders and the Chroococcales, respectively. We also describe 3 conserved indels in flavoprotein, heme oxygenase and protochlorophyllide oxidoreductase proteins that are specific for either Clade C cyanobacteria or for various subclades of Prochlorococcus. Many other conserved indels for cyanobacterial clades have been described recently.

Conclusions: These signature proteins and indels provide novel means for circumscription of various cyanobacterial clades in clear molecular terms. Their functional studies should lead to discovery of novel properties that are unique to these groups of cyanobacteria.

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Partial sequence alignment of the protein protochlorophyllide oxidoreductase showing a 1 aa deletion that is commonly shared by all Prochlorococcus strains except MIT 9303 and MIT 9313. This indel provides evidence for the deep branching of these Prochlorococcus strains relative to all other strains.
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Figure 5: Partial sequence alignment of the protein protochlorophyllide oxidoreductase showing a 1 aa deletion that is commonly shared by all Prochlorococcus strains except MIT 9303 and MIT 9313. This indel provides evidence for the deep branching of these Prochlorococcus strains relative to all other strains.

Mentions: As noted above, in phylogenetic trees based on concatenated protein sequences Prochlorococcus str. MIT9303 and MIT9313 branch within the various Synechococcus strains/isolates (Fig. 1 and additional file 2). Earlier phylogenetic studies by Rocap et al. [41] based on the 16S-23S rDNA spacer region indicate that these two strains (high B/A clade IV) form the deepest branching isolates of this genus. Further, in contrast to other sequenced Prochlorococcus strains, whose G+C content range from 30-39%, the strains MIT9303 and MIT9313 have much higher G+C content (~50%) (see Table 1). Our blast analyses, in addition to identifying many proteins that are unique to various Synechococcus strains/isolates, have also identified 22 proteins that are specifically present in all of the Clade C Synechococcus strains as well as in Prochlorococcus MIT9303 and MIT9313 (additional file 6a). At the same time, we have come across 37 proteins that are uniquely found in all other sequenced Prochlorococcus strains, but which are missing in MIT9303 and MIT9313 (additional file 6b). In addition, we have also identified a 1 aa deletion in a conserved region of the protein protochlorophyllide oxidoreductase (POR) that is uniquely shared by all other Prochlorococcus strains except MIT9303 and MIT9313 (Fig. 5). The enzyme POR is responsible for catalyzing light driven reduction of protochlorophyllide to chlorophyllide - a key regulatory reaction in the chlorophyll biosynthetic pathway [55]. Hence, it is again of much interest to understand the functional significance of this conserved indel. The rare genetic change leading to this indel likely occurred in a common ancestor of various Prochlorococcus strains after the branching of MIT9303 and MIT9313 (Fig. 2). These observations, in conjunction with the branching pattern of these strains in phylogenetic trees, provide evidence that these two Prochlorococcus strains comprise the deepest branching group (high B/A clade IV) [41] within the Prochlorococcus genus, exhibiting closest relationship to the Synechococcus strains/isolates.


Signature proteins for the major clades of Cyanobacteria.

Gupta RS, Mathews DW - BMC Evol. Biol. (2010)

Partial sequence alignment of the protein protochlorophyllide oxidoreductase showing a 1 aa deletion that is commonly shared by all Prochlorococcus strains except MIT 9303 and MIT 9313. This indel provides evidence for the deep branching of these Prochlorococcus strains relative to all other strains.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2823733&req=5

Figure 5: Partial sequence alignment of the protein protochlorophyllide oxidoreductase showing a 1 aa deletion that is commonly shared by all Prochlorococcus strains except MIT 9303 and MIT 9313. This indel provides evidence for the deep branching of these Prochlorococcus strains relative to all other strains.
Mentions: As noted above, in phylogenetic trees based on concatenated protein sequences Prochlorococcus str. MIT9303 and MIT9313 branch within the various Synechococcus strains/isolates (Fig. 1 and additional file 2). Earlier phylogenetic studies by Rocap et al. [41] based on the 16S-23S rDNA spacer region indicate that these two strains (high B/A clade IV) form the deepest branching isolates of this genus. Further, in contrast to other sequenced Prochlorococcus strains, whose G+C content range from 30-39%, the strains MIT9303 and MIT9313 have much higher G+C content (~50%) (see Table 1). Our blast analyses, in addition to identifying many proteins that are unique to various Synechococcus strains/isolates, have also identified 22 proteins that are specifically present in all of the Clade C Synechococcus strains as well as in Prochlorococcus MIT9303 and MIT9313 (additional file 6a). At the same time, we have come across 37 proteins that are uniquely found in all other sequenced Prochlorococcus strains, but which are missing in MIT9303 and MIT9313 (additional file 6b). In addition, we have also identified a 1 aa deletion in a conserved region of the protein protochlorophyllide oxidoreductase (POR) that is uniquely shared by all other Prochlorococcus strains except MIT9303 and MIT9313 (Fig. 5). The enzyme POR is responsible for catalyzing light driven reduction of protochlorophyllide to chlorophyllide - a key regulatory reaction in the chlorophyll biosynthetic pathway [55]. Hence, it is again of much interest to understand the functional significance of this conserved indel. The rare genetic change leading to this indel likely occurred in a common ancestor of various Prochlorococcus strains after the branching of MIT9303 and MIT9313 (Fig. 2). These observations, in conjunction with the branching pattern of these strains in phylogenetic trees, provide evidence that these two Prochlorococcus strains comprise the deepest branching group (high B/A clade IV) [41] within the Prochlorococcus genus, exhibiting closest relationship to the Synechococcus strains/isolates.

Bottom Line: We also describe 3 conserved indels in flavoprotein, heme oxygenase and protochlorophyllide oxidoreductase proteins that are specific for either Clade C cyanobacteria or for various subclades of Prochlorococcus.These signature proteins and indels provide novel means for circumscription of various cyanobacterial clades in clear molecular terms.Their functional studies should lead to discovery of novel properties that are unique to these groups of cyanobacteria.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada. gupta@mcmaster.ca

ABSTRACT

Background: The phylogeny and taxonomy of cyanobacteria is currently poorly understood due to paucity of reliable markers for identification and circumscription of its major clades.

Results: A combination of phylogenomic and protein signature based approaches was used to characterize the major clades of cyanobacteria. Phylogenetic trees were constructed for 44 cyanobacteria based on 44 conserved proteins. In parallel, Blastp searches were carried out on each ORF in the genomes of Synechococcus WH8102, Synechocystis PCC6803, Nostoc PCC7120, Synechococcus JA-3-3Ab, Prochlorococcus MIT9215 and Prochlor. marinus subsp. marinus CCMP1375 to identify proteins that are specific for various main clades of cyanobacteria. These studies have identified 39 proteins that are specific for all (or most) cyanobacteria and large numbers of proteins for other cyanobacterial clades. The identified signature proteins include: (i) 14 proteins for a deep branching clade (Clade A) of Gloebacter violaceus and two diazotrophic Synechococcus strains (JA-3-3Ab and JA2-3-B'a); (ii) 5 proteins that are present in all other cyanobacteria except those from Clade A; (iii) 60 proteins that are specific for a clade (Clade C) consisting of various marine unicellular cyanobacteria (viz. Synechococcus and Prochlorococcus); (iv) 14 and 19 signature proteins that are specific for the Clade C Synechococcus and Prochlorococcus strains, respectively; (v) 67 proteins that are specific for the Low B/A ecotype Prochlorococcus strains, containing lower ratio of chl b/a2 and adapted to growth at high light intensities; (vi) 65 and 8 proteins that are specific for the Nostocales and Chroococcales orders, respectively; and (vii) 22 and 9 proteins that are uniquely shared by various Nostocales and Oscillatoriales orders, or by these two orders and the Chroococcales, respectively. We also describe 3 conserved indels in flavoprotein, heme oxygenase and protochlorophyllide oxidoreductase proteins that are specific for either Clade C cyanobacteria or for various subclades of Prochlorococcus. Many other conserved indels for cyanobacterial clades have been described recently.

Conclusions: These signature proteins and indels provide novel means for circumscription of various cyanobacterial clades in clear molecular terms. Their functional studies should lead to discovery of novel properties that are unique to these groups of cyanobacteria.

Show MeSH