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Sucrose metabolism gene families and their biological functions.

Jiang SY, Chi YH, Wang JZ, Zhou JX, Cheng YS, Zhang BL, Ma A, Vanitha J, Ramachandran S - Sci Rep (2015)

Bottom Line: Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions.They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion.Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses.

View Article: PubMed Central - PubMed

Affiliation: Genome Structural Biology Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604.

ABSTRACT
Sucrose, as the main product of photosynthesis, plays crucial roles in plant development. Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions. We focused on four sucrose metabolism related gene families including sucrose synthase, sucrose phosphate synthase, sucrose phosphate phosphatase and UDP-glucose pyrophosphorylase. These gene families exhibited different expansion and evolutionary history as their host genomes experienced differentiated rates of the whole genome duplication, tandem and segmental duplication, or mobile element mediated gene gain and loss. They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion. However, we have detected recent positive selection during intra-species divergence. Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses. Our studies uncovered the molecular mechanisms of gene expansion and evolution and also provided new insight into the role of positive selection in intra-species divergence. Overexpression data revealed novel biological functions of these genes in flowering time control and seed germination under normal and stress conditions.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic analyses and evolutionary history of the SuSy, SPS, SPP and UDPGP families.(A–D) Phylogenetic analyses of the SuSy, SPS, SPP and UDPGP families, respectively, in 15 species including 4 monocot and 9 dicot plants as well as 1 spikemoss and 1 algae. Domain amino acid sequences were achieved to construct phylogenetic trees using the bootstrap method with a heuristic search of the PAUP 4.0 b8 program. The results were confirmed by the Bayesian analyses. We defined ancestral units according to the description by Shiu et al. (2004)38. Their enlarged phylogenetic trees are shown in Supplementary Fig. S2 (A–D), respectively. (E) Evolutionary history of the four gene families in 15 organisms. Black circles represent the MRCA units among all 15 organisms; blue triangles indicate the MRCA units among 14 embryophyte species and green squares show the MRCA units among angiosperm species. Red heart shapes and pink stars represent the MRCA units in 9 dicot and 4 monocot plants, respectively.
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f1: Phylogenetic analyses and evolutionary history of the SuSy, SPS, SPP and UDPGP families.(A–D) Phylogenetic analyses of the SuSy, SPS, SPP and UDPGP families, respectively, in 15 species including 4 monocot and 9 dicot plants as well as 1 spikemoss and 1 algae. Domain amino acid sequences were achieved to construct phylogenetic trees using the bootstrap method with a heuristic search of the PAUP 4.0 b8 program. The results were confirmed by the Bayesian analyses. We defined ancestral units according to the description by Shiu et al. (2004)38. Their enlarged phylogenetic trees are shown in Supplementary Fig. S2 (A–D), respectively. (E) Evolutionary history of the four gene families in 15 organisms. Black circles represent the MRCA units among all 15 organisms; blue triangles indicate the MRCA units among 14 embryophyte species and green squares show the MRCA units among angiosperm species. Red heart shapes and pink stars represent the MRCA units in 9 dicot and 4 monocot plants, respectively.

Mentions: To classify the members of these four gene families and to facilitate their functional analysis, we reconstructed the phylogenetic relationship in each family (Fig. 1A–D, Supplementary Fig. S2 A–D) using their corresponding protein domain sequences as described in the Methods. Previous studies identified 3 groups of SuSy genes, which were based on available SuSy members from limited plant species45. However, the phylogenetic tree based on SuSy members from 15 species showed that a total of 5 groups could be clustered (Fig. 1A and Supplementary Fig. S2A). Both groups I and II are the main groups consisting of members from all dicot and monocot plants. The remaining three groups are species-specific and they consist of members from limited species. For the SPS gene family, we identified 3 groups (Fig. 1B and Supplementary Fig. S2B). Among them, group I is the largest one, consisting of the all members from both dicot and monocot plants. Previous data showed that four groups were identified8. However, in the study, groups B and C were actually in the same group8; thus, similar to our result. On the other hand, the SPP family was also clustered into three different groups with the group I as the largest one consisting of all members from angiosperm species (Fig. 1C and Supplementary Fig. S2C). As for the UDPGP family, no genome-wide identification was previously reported. We have identified a total of 110 members from 15 species (Table 1) and they could be clustered into two groups (Fig. 1D and Supplementary Fig. S2D). In each group, at least one member has been included from all the 15 species.


Sucrose metabolism gene families and their biological functions.

Jiang SY, Chi YH, Wang JZ, Zhou JX, Cheng YS, Zhang BL, Ma A, Vanitha J, Ramachandran S - Sci Rep (2015)

Phylogenetic analyses and evolutionary history of the SuSy, SPS, SPP and UDPGP families.(A–D) Phylogenetic analyses of the SuSy, SPS, SPP and UDPGP families, respectively, in 15 species including 4 monocot and 9 dicot plants as well as 1 spikemoss and 1 algae. Domain amino acid sequences were achieved to construct phylogenetic trees using the bootstrap method with a heuristic search of the PAUP 4.0 b8 program. The results were confirmed by the Bayesian analyses. We defined ancestral units according to the description by Shiu et al. (2004)38. Their enlarged phylogenetic trees are shown in Supplementary Fig. S2 (A–D), respectively. (E) Evolutionary history of the four gene families in 15 organisms. Black circles represent the MRCA units among all 15 organisms; blue triangles indicate the MRCA units among 14 embryophyte species and green squares show the MRCA units among angiosperm species. Red heart shapes and pink stars represent the MRCA units in 9 dicot and 4 monocot plants, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4663468&req=5

f1: Phylogenetic analyses and evolutionary history of the SuSy, SPS, SPP and UDPGP families.(A–D) Phylogenetic analyses of the SuSy, SPS, SPP and UDPGP families, respectively, in 15 species including 4 monocot and 9 dicot plants as well as 1 spikemoss and 1 algae. Domain amino acid sequences were achieved to construct phylogenetic trees using the bootstrap method with a heuristic search of the PAUP 4.0 b8 program. The results were confirmed by the Bayesian analyses. We defined ancestral units according to the description by Shiu et al. (2004)38. Their enlarged phylogenetic trees are shown in Supplementary Fig. S2 (A–D), respectively. (E) Evolutionary history of the four gene families in 15 organisms. Black circles represent the MRCA units among all 15 organisms; blue triangles indicate the MRCA units among 14 embryophyte species and green squares show the MRCA units among angiosperm species. Red heart shapes and pink stars represent the MRCA units in 9 dicot and 4 monocot plants, respectively.
Mentions: To classify the members of these four gene families and to facilitate their functional analysis, we reconstructed the phylogenetic relationship in each family (Fig. 1A–D, Supplementary Fig. S2 A–D) using their corresponding protein domain sequences as described in the Methods. Previous studies identified 3 groups of SuSy genes, which were based on available SuSy members from limited plant species45. However, the phylogenetic tree based on SuSy members from 15 species showed that a total of 5 groups could be clustered (Fig. 1A and Supplementary Fig. S2A). Both groups I and II are the main groups consisting of members from all dicot and monocot plants. The remaining three groups are species-specific and they consist of members from limited species. For the SPS gene family, we identified 3 groups (Fig. 1B and Supplementary Fig. S2B). Among them, group I is the largest one, consisting of the all members from both dicot and monocot plants. Previous data showed that four groups were identified8. However, in the study, groups B and C were actually in the same group8; thus, similar to our result. On the other hand, the SPP family was also clustered into three different groups with the group I as the largest one consisting of all members from angiosperm species (Fig. 1C and Supplementary Fig. S2C). As for the UDPGP family, no genome-wide identification was previously reported. We have identified a total of 110 members from 15 species (Table 1) and they could be clustered into two groups (Fig. 1D and Supplementary Fig. S2D). In each group, at least one member has been included from all the 15 species.

Bottom Line: Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions.They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion.Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses.

View Article: PubMed Central - PubMed

Affiliation: Genome Structural Biology Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604.

ABSTRACT
Sucrose, as the main product of photosynthesis, plays crucial roles in plant development. Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions. We focused on four sucrose metabolism related gene families including sucrose synthase, sucrose phosphate synthase, sucrose phosphate phosphatase and UDP-glucose pyrophosphorylase. These gene families exhibited different expansion and evolutionary history as their host genomes experienced differentiated rates of the whole genome duplication, tandem and segmental duplication, or mobile element mediated gene gain and loss. They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion. However, we have detected recent positive selection during intra-species divergence. Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses. Our studies uncovered the molecular mechanisms of gene expansion and evolution and also provided new insight into the role of positive selection in intra-species divergence. Overexpression data revealed novel biological functions of these genes in flowering time control and seed germination under normal and stress conditions.

No MeSH data available.


Related in: MedlinePlus