Limits...
Duplications and functional divergence of ADP-glucose pyrophosphorylase genes in plants.

Georgelis N, Braun EL, Hannah LC - BMC Evol. Biol. (2008)

Bottom Line: We found that the first duplication in the AGPase large subunit family occurred early in the history of land plants, while the earliest small subunit duplication occurred after the divergence of monocots and eudicots.Instead, evolutionary constraints appear to be permanently relaxed for the large subunit relative to the small subunit.We discuss the phenotypes of mutants that alter some candidate sites and strategies for examining candidate sites of presently unknown function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Program in Plant Molecular and Cellular Biology and Horticultural Sciences, University of Florida, Gainesville, Florida 32610-0245, USA. gnick@ufl.edu

ABSTRACT

Background: ADP-glucose pyrophosphorylase (AGPase), which catalyses a rate limiting step in starch synthesis, is a heterotetramer comprised of two identical large and two identical small subunits in plants. Although the large and small subunits are equally sensitive to activity-altering amino acid changes when expressed in a bacterial system, the overall rate of non-synonymous evolution is approximately 2.7-fold greater for the large subunit than for the small subunit. Herein, we examine the basis for their different rates of evolution, the number of duplications in both large and small subunit genes and document changes in the patterns of AGPase evolution over time.

Results: We found that the first duplication in the AGPase large subunit family occurred early in the history of land plants, while the earliest small subunit duplication occurred after the divergence of monocots and eudicots. The large subunit also had a larger number of gene duplications than did the small subunit. The ancient duplications in the large subunit family raise concern about the saturation of synonymous substitutions, but estimates of the absolute rate of AGPase evolution were highly correlated with estimates of omega (the non-synonymous to synonymous rate ratio). Both subunits showed evidence for positive selection and relaxation of purifying selection after duplication, but these phenomena could not explain the different evolutionary rates of the two subunits. Instead, evolutionary constraints appear to be permanently relaxed for the large subunit relative to the small subunit. Both subunits exhibit branch-specific patterns of rate variation among sites.

Conclusion: These analyses indicate that the higher evolutionary rate of the plant AGPase large subunit reflects permanent relaxation of constraints relative to the small subunit and they show that the large subunit genes have undergone more gene duplications than small subunit genes. Candidate sites potentially responsible for functional divergence within each of the AGPase subunits were investigated by examining branch-specific patterns of rate variation. We discuss the phenotypes of mutants that alter some candidate sites and strategies for examining candidate sites of presently unknown function.

Show MeSH
Reconciled large and small subunit trees. A) Amino acid tree of the large and small subunits from angiosperms, Physcomitrella patens and Chlamydomonas reinhardtii. The topology of the tree was determined by ML using aligned amino acid sequences using PhyML. Branch lengths reflect numbers of amino acid substitutions per site. The branches within groups have been replaced by the grey triangles. ML bootstrap values are indicated above branches, and the bar shows the number of amino acid substitutions per site. B) Angiosperm large subunit reconciled tree. C) Angiosperm small subunit reconciled tree. The topology of the trees shown in B) and C) was determined by ML using aligned cDNA sequences using GARLI. Branch lengths reflect numbers of amino acid substitutions per site as estimated by AAML and the scale bar shows the number of amino acid substitutions per site. ML bootstrap values > 50% are indicated above branches. Reconciled tree analyses (using the gene trees shown and the species tree shown in Additional file 1) were conducted using GENETREE. Black boxes at nodes indicate duplication events. The arrow in B) indicates the divergence of Physcomitrella patens from angiosperms. The trees in B) and C) were rooted with the AGPase large and small subunit from Chlamydomonas reinhardtii respectively. Thicker lines indicate branches that follow duplication events and have KS < 0.1 (based upon ML estimates of synonymous branch lengths).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2529307&req=5

Figure 1: Reconciled large and small subunit trees. A) Amino acid tree of the large and small subunits from angiosperms, Physcomitrella patens and Chlamydomonas reinhardtii. The topology of the tree was determined by ML using aligned amino acid sequences using PhyML. Branch lengths reflect numbers of amino acid substitutions per site. The branches within groups have been replaced by the grey triangles. ML bootstrap values are indicated above branches, and the bar shows the number of amino acid substitutions per site. B) Angiosperm large subunit reconciled tree. C) Angiosperm small subunit reconciled tree. The topology of the trees shown in B) and C) was determined by ML using aligned cDNA sequences using GARLI. Branch lengths reflect numbers of amino acid substitutions per site as estimated by AAML and the scale bar shows the number of amino acid substitutions per site. ML bootstrap values > 50% are indicated above branches. Reconciled tree analyses (using the gene trees shown and the species tree shown in Additional file 1) were conducted using GENETREE. Black boxes at nodes indicate duplication events. The arrow in B) indicates the divergence of Physcomitrella patens from angiosperms. The trees in B) and C) were rooted with the AGPase large and small subunit from Chlamydomonas reinhardtii respectively. Thicker lines indicate branches that follow duplication events and have KS < 0.1 (based upon ML estimates of synonymous branch lengths).

Mentions: ADP-glucose pyrophosphorylase (AGPase; EC 2.7.7.27) catalyses a rate-limiting step in starch synthesis, the formation of ADP-glucose from glucose-1-P and ATP. ADP-glucose is the predominant, if not sole, precursor for starch synthesis. While AGPase is a homotetramer in bacteria (including cyanobacteria), it is a heterotetramer in angiosperms and green algae. This heterotetramer comprises two identical large and two identical small subunits. They exhibit a high degree of identity to each other and to the cyanobacterial AGPase, pointing to an origin by gene duplication early in the evolution of plants and green algae (Figure 1A) (Additional file 1) [1,2]. The two subunits have complementary rather than redundant functions, and knockout mutations in either abolish more than 90% of AGPase activity in some experimental systems [3].


Duplications and functional divergence of ADP-glucose pyrophosphorylase genes in plants.

Georgelis N, Braun EL, Hannah LC - BMC Evol. Biol. (2008)

Reconciled large and small subunit trees. A) Amino acid tree of the large and small subunits from angiosperms, Physcomitrella patens and Chlamydomonas reinhardtii. The topology of the tree was determined by ML using aligned amino acid sequences using PhyML. Branch lengths reflect numbers of amino acid substitutions per site. The branches within groups have been replaced by the grey triangles. ML bootstrap values are indicated above branches, and the bar shows the number of amino acid substitutions per site. B) Angiosperm large subunit reconciled tree. C) Angiosperm small subunit reconciled tree. The topology of the trees shown in B) and C) was determined by ML using aligned cDNA sequences using GARLI. Branch lengths reflect numbers of amino acid substitutions per site as estimated by AAML and the scale bar shows the number of amino acid substitutions per site. ML bootstrap values > 50% are indicated above branches. Reconciled tree analyses (using the gene trees shown and the species tree shown in Additional file 1) were conducted using GENETREE. Black boxes at nodes indicate duplication events. The arrow in B) indicates the divergence of Physcomitrella patens from angiosperms. The trees in B) and C) were rooted with the AGPase large and small subunit from Chlamydomonas reinhardtii respectively. Thicker lines indicate branches that follow duplication events and have KS < 0.1 (based upon ML estimates of synonymous branch lengths).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2529307&req=5

Figure 1: Reconciled large and small subunit trees. A) Amino acid tree of the large and small subunits from angiosperms, Physcomitrella patens and Chlamydomonas reinhardtii. The topology of the tree was determined by ML using aligned amino acid sequences using PhyML. Branch lengths reflect numbers of amino acid substitutions per site. The branches within groups have been replaced by the grey triangles. ML bootstrap values are indicated above branches, and the bar shows the number of amino acid substitutions per site. B) Angiosperm large subunit reconciled tree. C) Angiosperm small subunit reconciled tree. The topology of the trees shown in B) and C) was determined by ML using aligned cDNA sequences using GARLI. Branch lengths reflect numbers of amino acid substitutions per site as estimated by AAML and the scale bar shows the number of amino acid substitutions per site. ML bootstrap values > 50% are indicated above branches. Reconciled tree analyses (using the gene trees shown and the species tree shown in Additional file 1) were conducted using GENETREE. Black boxes at nodes indicate duplication events. The arrow in B) indicates the divergence of Physcomitrella patens from angiosperms. The trees in B) and C) were rooted with the AGPase large and small subunit from Chlamydomonas reinhardtii respectively. Thicker lines indicate branches that follow duplication events and have KS < 0.1 (based upon ML estimates of synonymous branch lengths).
Mentions: ADP-glucose pyrophosphorylase (AGPase; EC 2.7.7.27) catalyses a rate-limiting step in starch synthesis, the formation of ADP-glucose from glucose-1-P and ATP. ADP-glucose is the predominant, if not sole, precursor for starch synthesis. While AGPase is a homotetramer in bacteria (including cyanobacteria), it is a heterotetramer in angiosperms and green algae. This heterotetramer comprises two identical large and two identical small subunits. They exhibit a high degree of identity to each other and to the cyanobacterial AGPase, pointing to an origin by gene duplication early in the evolution of plants and green algae (Figure 1A) (Additional file 1) [1,2]. The two subunits have complementary rather than redundant functions, and knockout mutations in either abolish more than 90% of AGPase activity in some experimental systems [3].

Bottom Line: We found that the first duplication in the AGPase large subunit family occurred early in the history of land plants, while the earliest small subunit duplication occurred after the divergence of monocots and eudicots.Instead, evolutionary constraints appear to be permanently relaxed for the large subunit relative to the small subunit.We discuss the phenotypes of mutants that alter some candidate sites and strategies for examining candidate sites of presently unknown function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Program in Plant Molecular and Cellular Biology and Horticultural Sciences, University of Florida, Gainesville, Florida 32610-0245, USA. gnick@ufl.edu

ABSTRACT

Background: ADP-glucose pyrophosphorylase (AGPase), which catalyses a rate limiting step in starch synthesis, is a heterotetramer comprised of two identical large and two identical small subunits in plants. Although the large and small subunits are equally sensitive to activity-altering amino acid changes when expressed in a bacterial system, the overall rate of non-synonymous evolution is approximately 2.7-fold greater for the large subunit than for the small subunit. Herein, we examine the basis for their different rates of evolution, the number of duplications in both large and small subunit genes and document changes in the patterns of AGPase evolution over time.

Results: We found that the first duplication in the AGPase large subunit family occurred early in the history of land plants, while the earliest small subunit duplication occurred after the divergence of monocots and eudicots. The large subunit also had a larger number of gene duplications than did the small subunit. The ancient duplications in the large subunit family raise concern about the saturation of synonymous substitutions, but estimates of the absolute rate of AGPase evolution were highly correlated with estimates of omega (the non-synonymous to synonymous rate ratio). Both subunits showed evidence for positive selection and relaxation of purifying selection after duplication, but these phenomena could not explain the different evolutionary rates of the two subunits. Instead, evolutionary constraints appear to be permanently relaxed for the large subunit relative to the small subunit. Both subunits exhibit branch-specific patterns of rate variation among sites.

Conclusion: These analyses indicate that the higher evolutionary rate of the plant AGPase large subunit reflects permanent relaxation of constraints relative to the small subunit and they show that the large subunit genes have undergone more gene duplications than small subunit genes. Candidate sites potentially responsible for functional divergence within each of the AGPase subunits were investigated by examining branch-specific patterns of rate variation. We discuss the phenotypes of mutants that alter some candidate sites and strategies for examining candidate sites of presently unknown function.

Show MeSH