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Advances in Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component.

Cai F, Dou Z, Bernstein SL, Leverenz R, Williams EB, Heinhorst S, Shively J, Cannon GC, Kerfeld CA - Life (Basel) (2015)

Bottom Line: Two types of carboxysome, α and β, encapsulating form IA and form IB d-ribulose-1,5-bisphosphate carboxylase/oxygenase, respectively, differ in gene organization and associated proteins.Based on our results from bioinformatic, biophysical, genetic and biochemical approaches, including peptide array scanning for protein-protein interactions, we propose a model for CsoS2 function and its spatial location in the α-carboxysome.Analogies between the pathway for β-carboxysome biogenesis and our model for α-carboxysome assembly are discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA. fcai@lbl.gov.

ABSTRACT
The marine Synechococcus and Prochlorococcus are the numerically dominant cyanobacteria in the ocean and important in global carbon fixation. They have evolved a CO2-concentrating-mechanism, of which the central component is the carboxysome, a self-assembling proteinaceous organelle. Two types of carboxysome, α and β, encapsulating form IA and form IB d-ribulose-1,5-bisphosphate carboxylase/oxygenase, respectively, differ in gene organization and associated proteins. In contrast to the β-carboxysome, the assembly process of the α-carboxysome is enigmatic. Moreover, an absolutely conserved α-carboxysome protein, CsoS2, is of unknown function and has proven recalcitrant to crystallization. Here, we present studies on the CsoS2 protein in three model organisms and show that CsoS2 is vital for α-carboxysome biogenesis. The primary structure of CsoS2 appears tripartite, composed of an N-terminal, middle (M)-, and C-terminal region. Repetitive motifs can be identified in the N- and M-regions. Multiple lines of evidence suggest CsoS2 is highly flexible, possibly an intrinsically disordered protein. Based on our results from bioinformatic, biophysical, genetic and biochemical approaches, including peptide array scanning for protein-protein interactions, we propose a model for CsoS2 function and its spatial location in the α-carboxysome. Analogies between the pathway for β-carboxysome biogenesis and our model for α-carboxysome assembly are discussed.

No MeSH data available.


A CsoS2 phylogram. CsoS2 orthologs (Table S2) found in α-Cyanobacteria (green), α-Proteobacteria (blue), β-Proteobacteria (orange), γ-Proteobacteria (black), Actinobacteria (red) and Nitrospirae (magenta) are shown in the phylogram. Purple phototrophs, which belong to the γ-Proteobacteria, are shown in purple. Bootstrap values were obtained from 100 replicates; nodes receiving bootstrap values greater than 75 or between 50 and 74 are indicated by filled circles or filled triangles, respectively. Numbers correspond to organism ID numbers given in Table S2.
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life-05-01141-f007: A CsoS2 phylogram. CsoS2 orthologs (Table S2) found in α-Cyanobacteria (green), α-Proteobacteria (blue), β-Proteobacteria (orange), γ-Proteobacteria (black), Actinobacteria (red) and Nitrospirae (magenta) are shown in the phylogram. Purple phototrophs, which belong to the γ-Proteobacteria, are shown in purple. Bootstrap values were obtained from 100 replicates; nodes receiving bootstrap values greater than 75 or between 50 and 74 are indicated by filled circles or filled triangles, respectively. Numbers correspond to organism ID numbers given in Table S2.

Mentions: A phylogenetic tree based on the maximum-likelihood method with 100 Bootstrap (bs) replicates was constructed using all CsoS2 orthologs. CsoS2 orthologs from the Cyanobacteria form a single clade (bs = 90%), while CsoS2s from purple phototrophs form at least two clades (bs = 90% and 50%), one being a sister clade of the Cyanobacterial CsoS2. The topology of the CsoS2 tree is different from that of the bacterial phyla tree [29], and it suggests that CsoS2 may have first occurred in the common ancestor of the Proteobacteria (Figure 7). The possibility that α-cyanobacteria obtained α-carboxysomes via a horizontal gene transfer (HGT) event from Proteobacteria has been proposed [30,31]. This hypothesis is also consistent with the absence of either α- or β-carboxysomal genes in bacterial genomes belonging to Melainabacteria, a sibling phylum sharing a common ancestor with both α- and β-cyanobacteria [32]. Possible HGT events are also evident in the cases of α-carboxysome containing genomes belonging to Actinobacteria and Nitrospiare (namely, Acidimicrobium ferrooxidans DSM 10331 and Leptospirillum ferriphilum BYQ, respectively) (Figure 7).


Advances in Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component.

Cai F, Dou Z, Bernstein SL, Leverenz R, Williams EB, Heinhorst S, Shively J, Cannon GC, Kerfeld CA - Life (Basel) (2015)

A CsoS2 phylogram. CsoS2 orthologs (Table S2) found in α-Cyanobacteria (green), α-Proteobacteria (blue), β-Proteobacteria (orange), γ-Proteobacteria (black), Actinobacteria (red) and Nitrospirae (magenta) are shown in the phylogram. Purple phototrophs, which belong to the γ-Proteobacteria, are shown in purple. Bootstrap values were obtained from 100 replicates; nodes receiving bootstrap values greater than 75 or between 50 and 74 are indicated by filled circles or filled triangles, respectively. Numbers correspond to organism ID numbers given in Table S2.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4499774&req=5

life-05-01141-f007: A CsoS2 phylogram. CsoS2 orthologs (Table S2) found in α-Cyanobacteria (green), α-Proteobacteria (blue), β-Proteobacteria (orange), γ-Proteobacteria (black), Actinobacteria (red) and Nitrospirae (magenta) are shown in the phylogram. Purple phototrophs, which belong to the γ-Proteobacteria, are shown in purple. Bootstrap values were obtained from 100 replicates; nodes receiving bootstrap values greater than 75 or between 50 and 74 are indicated by filled circles or filled triangles, respectively. Numbers correspond to organism ID numbers given in Table S2.
Mentions: A phylogenetic tree based on the maximum-likelihood method with 100 Bootstrap (bs) replicates was constructed using all CsoS2 orthologs. CsoS2 orthologs from the Cyanobacteria form a single clade (bs = 90%), while CsoS2s from purple phototrophs form at least two clades (bs = 90% and 50%), one being a sister clade of the Cyanobacterial CsoS2. The topology of the CsoS2 tree is different from that of the bacterial phyla tree [29], and it suggests that CsoS2 may have first occurred in the common ancestor of the Proteobacteria (Figure 7). The possibility that α-cyanobacteria obtained α-carboxysomes via a horizontal gene transfer (HGT) event from Proteobacteria has been proposed [30,31]. This hypothesis is also consistent with the absence of either α- or β-carboxysomal genes in bacterial genomes belonging to Melainabacteria, a sibling phylum sharing a common ancestor with both α- and β-cyanobacteria [32]. Possible HGT events are also evident in the cases of α-carboxysome containing genomes belonging to Actinobacteria and Nitrospiare (namely, Acidimicrobium ferrooxidans DSM 10331 and Leptospirillum ferriphilum BYQ, respectively) (Figure 7).

Bottom Line: Two types of carboxysome, α and β, encapsulating form IA and form IB d-ribulose-1,5-bisphosphate carboxylase/oxygenase, respectively, differ in gene organization and associated proteins.Based on our results from bioinformatic, biophysical, genetic and biochemical approaches, including peptide array scanning for protein-protein interactions, we propose a model for CsoS2 function and its spatial location in the α-carboxysome.Analogies between the pathway for β-carboxysome biogenesis and our model for α-carboxysome assembly are discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA. fcai@lbl.gov.

ABSTRACT
The marine Synechococcus and Prochlorococcus are the numerically dominant cyanobacteria in the ocean and important in global carbon fixation. They have evolved a CO2-concentrating-mechanism, of which the central component is the carboxysome, a self-assembling proteinaceous organelle. Two types of carboxysome, α and β, encapsulating form IA and form IB d-ribulose-1,5-bisphosphate carboxylase/oxygenase, respectively, differ in gene organization and associated proteins. In contrast to the β-carboxysome, the assembly process of the α-carboxysome is enigmatic. Moreover, an absolutely conserved α-carboxysome protein, CsoS2, is of unknown function and has proven recalcitrant to crystallization. Here, we present studies on the CsoS2 protein in three model organisms and show that CsoS2 is vital for α-carboxysome biogenesis. The primary structure of CsoS2 appears tripartite, composed of an N-terminal, middle (M)-, and C-terminal region. Repetitive motifs can be identified in the N- and M-regions. Multiple lines of evidence suggest CsoS2 is highly flexible, possibly an intrinsically disordered protein. Based on our results from bioinformatic, biophysical, genetic and biochemical approaches, including peptide array scanning for protein-protein interactions, we propose a model for CsoS2 function and its spatial location in the α-carboxysome. Analogies between the pathway for β-carboxysome biogenesis and our model for α-carboxysome assembly are discussed.

No MeSH data available.