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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 flavoprotein showing a 6 aa conserved insert (boxed) that is specific for the Clade C cyanobacteria. Dashes (-) in this and all other sequence alignments indicate identity with the amino acid on the top line. The numbers on the top indicate the position of the sequence in the species on the first line. The absence of this insert in all other cyanobacteria and other phyla of bacteria provide evidence that this indel is an insert in the Clade C.
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Figure 3: Partial sequence alignment of flavoprotein showing a 6 aa conserved insert (boxed) that is specific for the Clade C cyanobacteria. Dashes (-) in this and all other sequence alignments indicate identity with the amino acid on the top line. The numbers on the top indicate the position of the sequence in the species on the first line. The absence of this insert in all other cyanobacteria and other phyla of bacteria provide evidence that this indel is an insert in the Clade C.

Mentions: The Clade C is comprised of different strains/isolates of marine Prochlorococcus and Synechococcus [40,41,51-53]. We have recently described a number of conserved indels in widely distributed proteins that are specific for all of the species/strains from Clade C [23]. These signatures include a 3 aa insert in the RNA polymerase beta subunit, a 2 aa insert the proteins KsgA, a 6 aa insert in tyrosyl-tRNA synthetase, a 2 aa insert in the tRNA (guanine-N1-)-methyltransferase, a 1 aa insert in the RNA polymerase β' subunit and a 12 aa insert in the DNA polymerase I [23]. These signature indels are not found in the Clades A or B cyanobacteria or other phyla of bacteria. Additionally, they are also absent in Syn. elongatus as well as Synechococcus sps. PCC7002 and PCC7335. Another example of a signature insert that is specific for Clade C species/strains is presented in Fig. 3. In this case, a 6 aa insert in a flavoprotein is commonly present in all Clade C species/strains, but absent from all other cyanobacteria as well as other bacteria. This latter observation indicates that this indels is an insert in the Clade C species/strains. Interestingly, this insert and also several of the other Clade C signature indels are also present in Cyanobium sp. PCC7001 (Fig. 3), supporting its placement within the Clade C (Fig. 2) [4,15].


Signature proteins for the major clades of Cyanobacteria.

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

Partial sequence alignment of flavoprotein showing a 6 aa conserved insert (boxed) that is specific for the Clade C cyanobacteria. Dashes (-) in this and all other sequence alignments indicate identity with the amino acid on the top line. The numbers on the top indicate the position of the sequence in the species on the first line. The absence of this insert in all other cyanobacteria and other phyla of bacteria provide evidence that this indel is an insert in the Clade C.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Partial sequence alignment of flavoprotein showing a 6 aa conserved insert (boxed) that is specific for the Clade C cyanobacteria. Dashes (-) in this and all other sequence alignments indicate identity with the amino acid on the top line. The numbers on the top indicate the position of the sequence in the species on the first line. The absence of this insert in all other cyanobacteria and other phyla of bacteria provide evidence that this indel is an insert in the Clade C.
Mentions: The Clade C is comprised of different strains/isolates of marine Prochlorococcus and Synechococcus [40,41,51-53]. We have recently described a number of conserved indels in widely distributed proteins that are specific for all of the species/strains from Clade C [23]. These signatures include a 3 aa insert in the RNA polymerase beta subunit, a 2 aa insert the proteins KsgA, a 6 aa insert in tyrosyl-tRNA synthetase, a 2 aa insert in the tRNA (guanine-N1-)-methyltransferase, a 1 aa insert in the RNA polymerase β' subunit and a 12 aa insert in the DNA polymerase I [23]. These signature indels are not found in the Clades A or B cyanobacteria or other phyla of bacteria. Additionally, they are also absent in Syn. elongatus as well as Synechococcus sps. PCC7002 and PCC7335. Another example of a signature insert that is specific for Clade C species/strains is presented in Fig. 3. In this case, a 6 aa insert in a flavoprotein is commonly present in all Clade C species/strains, but absent from all other cyanobacteria as well as other bacteria. This latter observation indicates that this indels is an insert in the Clade C species/strains. Interestingly, this insert and also several of the other Clade C signature indels are also present in Cyanobium sp. PCC7001 (Fig. 3), supporting its placement within the Clade C (Fig. 2) [4,15].

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
Related in: MedlinePlus