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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.


Schematic of α-carboxysome gene organization in three model organisms. Locus boundaries are based on the LoClass algorithm for BMCclassification [4]. Conserved cso genes are color-coded: Bacterial Microcompartment domain (BMC; pfam00936)-containing genes (csoS1s) in orange; RuBisCO large and small subunits (cbbL/S) in dark and light green, respectively; csoS2 in red; carbonic anhydrase (csoS3) in purple; genes belong to pfam03319 (csoS4A/B) in yellow; and genes encoding pterin-4 alpha-carbinolamine dehydratase-like protein (PCD-like) in magenta. Gray-blue genes are shared within the BMC locus subtype; gray genes are shared with at least one other BMC locus type; white genes indicate that this gene is not considered part of the locus [4]. Annotations for gray-blue or gray coded genes are as following: 1. por (protochlorophyllide oxidoreductase); 2. chlL (light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein); 3. chlB (light-independent protochlorophyllide reductase subunit B); 4. chlN (light-independent protochlorophyllide reductase subunit N); 5. HAM1; 6. sbtA (high-affinity bicarbonate transporter); 7. sbtB (or annotated as nitrogen regulatory protein P-II); 8. cbiA (cobyrinic acid a,c-diamide synthase); 9. vwfA (von Willebrand factor type A); 10. nuoL (NADH-quinone oxidoreductase subunit L); 11. conserved gene with unknown function DUF2309 and 12. cbbQ (a putative catalytic chaperone of RuBisCO). Details on the gene organization of the subtypes of the α-carboxysome among all sequenced cyanobacterial genomes are also reviewed in Roberts et al. 2012 [8].
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life-05-01141-f001: Schematic of α-carboxysome gene organization in three model organisms. Locus boundaries are based on the LoClass algorithm for BMCclassification [4]. Conserved cso genes are color-coded: Bacterial Microcompartment domain (BMC; pfam00936)-containing genes (csoS1s) in orange; RuBisCO large and small subunits (cbbL/S) in dark and light green, respectively; csoS2 in red; carbonic anhydrase (csoS3) in purple; genes belong to pfam03319 (csoS4A/B) in yellow; and genes encoding pterin-4 alpha-carbinolamine dehydratase-like protein (PCD-like) in magenta. Gray-blue genes are shared within the BMC locus subtype; gray genes are shared with at least one other BMC locus type; white genes indicate that this gene is not considered part of the locus [4]. Annotations for gray-blue or gray coded genes are as following: 1. por (protochlorophyllide oxidoreductase); 2. chlL (light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein); 3. chlB (light-independent protochlorophyllide reductase subunit B); 4. chlN (light-independent protochlorophyllide reductase subunit N); 5. HAM1; 6. sbtA (high-affinity bicarbonate transporter); 7. sbtB (or annotated as nitrogen regulatory protein P-II); 8. cbiA (cobyrinic acid a,c-diamide synthase); 9. vwfA (von Willebrand factor type A); 10. nuoL (NADH-quinone oxidoreductase subunit L); 11. conserved gene with unknown function DUF2309 and 12. cbbQ (a putative catalytic chaperone of RuBisCO). Details on the gene organization of the subtypes of the α-carboxysome among all sequenced cyanobacterial genomes are also reviewed in Roberts et al. 2012 [8].

Mentions: Alpha- and β-carboxysomes also differ in gene organization. While the core genes of the α-type are organized in an operon (the cso operon) (Figure 1), genes of the β-type are located in a conserved locus (the ccm cluster) as well as in a few satellite loci [4]. Interestingly, while the β-carboxysome is exclusively found in β-cyanobacteria, the α-carboxysome can be found in not only α-cyanobacteria but also many chemoautotrophs. A cso operon was also found in the genome of the eukaryotic alga Paulinella chromatophora, a result of a horizontal gene transfer event [5]. Halothiobacillus neapolitanus (Hnea), a chemoautotroph, has served as a model organism for studying function and structure of the α-carboxysome [6]. Gene organization of cso operons from Hnea, Prochlorococcus marinus str. MED4 (MED4), a high-light adapted strain, and Prochlorococcus marinus str. MIT9313 (MIT9313), a low-light adapted strain, are shown in Figure 1. Gene(s) encoding the major shell proteins CsoS1 (containing one Bacterial Microcompartment (BMC) domain, pfam00936) is either the first or last gene(s) of the cso operon. The genes cbbL and cbbS code for the RuBisCO large and small subunits, respectively, followed by genes csoS2 and a gene encoding a β-class CA, csoS3. A pair of paralogous genes, csoS4A and csoS4B, encode the pentameric vertex proteins (pfam03319) of the carboxysome shell [7]. A gene containing a single BMC domain but with an N-terminal extension (80 to 100 amino acids) of unknown function, csoS1E, is unique to α-cyanobacteria, but not found in high-light adapted strains [8]. A gene encoding pterin-4 alpha-carbinolamine dehydratase-like protein is conserved in all known cso clusters [4,8,9]. Although it has been proposed as a novel RuBisCO chaperone [9], its absence has no effect on α-carboxysome function as a CO2-fixing module in a heterologous host [10]. The product of csoS1D, a tandem BMC domain containing gene, has been shown to be a minor component of α-carboxysomes from MED4 [8]. Wildtype and mutant α-carboxysomes can be readily purified to homogeneity from Hnea, providing insights on organelle function, protein composition, stoichiometry, and sub-structure localization [6,11,12,13,14]. Furthermore, in the last decade structures of most of the known α-carboxysome proteins were solved [7,15,16,17,18,19]. However, there is an essential piece missing from the model of the α-carboxysome: little is known about function and structure of the product of the csoS2 gene.


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)

Schematic of α-carboxysome gene organization in three model organisms. Locus boundaries are based on the LoClass algorithm for BMCclassification [4]. Conserved cso genes are color-coded: Bacterial Microcompartment domain (BMC; pfam00936)-containing genes (csoS1s) in orange; RuBisCO large and small subunits (cbbL/S) in dark and light green, respectively; csoS2 in red; carbonic anhydrase (csoS3) in purple; genes belong to pfam03319 (csoS4A/B) in yellow; and genes encoding pterin-4 alpha-carbinolamine dehydratase-like protein (PCD-like) in magenta. Gray-blue genes are shared within the BMC locus subtype; gray genes are shared with at least one other BMC locus type; white genes indicate that this gene is not considered part of the locus [4]. Annotations for gray-blue or gray coded genes are as following: 1. por (protochlorophyllide oxidoreductase); 2. chlL (light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein); 3. chlB (light-independent protochlorophyllide reductase subunit B); 4. chlN (light-independent protochlorophyllide reductase subunit N); 5. HAM1; 6. sbtA (high-affinity bicarbonate transporter); 7. sbtB (or annotated as nitrogen regulatory protein P-II); 8. cbiA (cobyrinic acid a,c-diamide synthase); 9. vwfA (von Willebrand factor type A); 10. nuoL (NADH-quinone oxidoreductase subunit L); 11. conserved gene with unknown function DUF2309 and 12. cbbQ (a putative catalytic chaperone of RuBisCO). Details on the gene organization of the subtypes of the α-carboxysome among all sequenced cyanobacterial genomes are also reviewed in Roberts et al. 2012 [8].
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Related In: Results  -  Collection

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life-05-01141-f001: Schematic of α-carboxysome gene organization in three model organisms. Locus boundaries are based on the LoClass algorithm for BMCclassification [4]. Conserved cso genes are color-coded: Bacterial Microcompartment domain (BMC; pfam00936)-containing genes (csoS1s) in orange; RuBisCO large and small subunits (cbbL/S) in dark and light green, respectively; csoS2 in red; carbonic anhydrase (csoS3) in purple; genes belong to pfam03319 (csoS4A/B) in yellow; and genes encoding pterin-4 alpha-carbinolamine dehydratase-like protein (PCD-like) in magenta. Gray-blue genes are shared within the BMC locus subtype; gray genes are shared with at least one other BMC locus type; white genes indicate that this gene is not considered part of the locus [4]. Annotations for gray-blue or gray coded genes are as following: 1. por (protochlorophyllide oxidoreductase); 2. chlL (light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein); 3. chlB (light-independent protochlorophyllide reductase subunit B); 4. chlN (light-independent protochlorophyllide reductase subunit N); 5. HAM1; 6. sbtA (high-affinity bicarbonate transporter); 7. sbtB (or annotated as nitrogen regulatory protein P-II); 8. cbiA (cobyrinic acid a,c-diamide synthase); 9. vwfA (von Willebrand factor type A); 10. nuoL (NADH-quinone oxidoreductase subunit L); 11. conserved gene with unknown function DUF2309 and 12. cbbQ (a putative catalytic chaperone of RuBisCO). Details on the gene organization of the subtypes of the α-carboxysome among all sequenced cyanobacterial genomes are also reviewed in Roberts et al. 2012 [8].
Mentions: Alpha- and β-carboxysomes also differ in gene organization. While the core genes of the α-type are organized in an operon (the cso operon) (Figure 1), genes of the β-type are located in a conserved locus (the ccm cluster) as well as in a few satellite loci [4]. Interestingly, while the β-carboxysome is exclusively found in β-cyanobacteria, the α-carboxysome can be found in not only α-cyanobacteria but also many chemoautotrophs. A cso operon was also found in the genome of the eukaryotic alga Paulinella chromatophora, a result of a horizontal gene transfer event [5]. Halothiobacillus neapolitanus (Hnea), a chemoautotroph, has served as a model organism for studying function and structure of the α-carboxysome [6]. Gene organization of cso operons from Hnea, Prochlorococcus marinus str. MED4 (MED4), a high-light adapted strain, and Prochlorococcus marinus str. MIT9313 (MIT9313), a low-light adapted strain, are shown in Figure 1. Gene(s) encoding the major shell proteins CsoS1 (containing one Bacterial Microcompartment (BMC) domain, pfam00936) is either the first or last gene(s) of the cso operon. The genes cbbL and cbbS code for the RuBisCO large and small subunits, respectively, followed by genes csoS2 and a gene encoding a β-class CA, csoS3. A pair of paralogous genes, csoS4A and csoS4B, encode the pentameric vertex proteins (pfam03319) of the carboxysome shell [7]. A gene containing a single BMC domain but with an N-terminal extension (80 to 100 amino acids) of unknown function, csoS1E, is unique to α-cyanobacteria, but not found in high-light adapted strains [8]. A gene encoding pterin-4 alpha-carbinolamine dehydratase-like protein is conserved in all known cso clusters [4,8,9]. Although it has been proposed as a novel RuBisCO chaperone [9], its absence has no effect on α-carboxysome function as a CO2-fixing module in a heterologous host [10]. The product of csoS1D, a tandem BMC domain containing gene, has been shown to be a minor component of α-carboxysomes from MED4 [8]. Wildtype and mutant α-carboxysomes can be readily purified to homogeneity from Hnea, providing insights on organelle function, protein composition, stoichiometry, and sub-structure localization [6,11,12,13,14]. Furthermore, in the last decade structures of most of the known α-carboxysome proteins were solved [7,15,16,17,18,19]. However, there is an essential piece missing from the model of the α-carboxysome: little is known about function and structure of the product of the csoS2 gene.

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.