Os07g0616800

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characteristic

The current work confirms that six genes comprise the entire rice Sucrose synthase (SUS) gene family.

picture1. Rice Sus gene family is comprised of six genes (from reference ).

It is obvious to note that each of the SUS genes is present on a separate chromosome, except SUS1 and 4 which are both located on chromosome. SUS3 is situated on chromosome 7. Analysis of gene structure for the six rice Sus genes

picture2. Analysis of gene structure for the six rice Sus genes (from reference ).

revealed that the genes typically consist of 14 or 15 exons. SUS3 is consisted of 15 exons similar to SUS2 and SUS4. Properties of the six predicted rice Sus proteins are shown in picture3.

picture3. Properties of the six predicted rice Sus proteins (from reference ).

A multiple sequence alignment analysis of the six rice sequences with Sus peptide sequences from other plant species revealed that the six rice Sus peptides can be classified into the three groups as suggested by Komatsu et al., namely Sus1 group (SUS1, 2 and 3), SusA group (SUS4), New Group (NG;SUS5 and 6). The predicted molecular weights of the six polypeptides are very close ranging from 92.1 to 96.5 kDa, with SUS3 being 93.2kDa. High levels of similarity exist between the predicted amino acid sequences of SUS1-4, ranging between 89 and 68%. The similarity between SUS3 and SUS1, SUS2, SUS4, SUS5 SUS6 are 89%, 79%, 68%, 53%, 52%, respectively. The predicted isoelectric point of SUS3 is somewhat lower (pI 5.94) than those of the other family members which range from 6.03 (SUS6) to 7.73 (SUS5) except indistinguishably with SUS2 (pI 5.93).

Function

In higher plants sucrose is the major form in which carbohydrate is transported from photosynthetic source tissues to sink tissues, and its subsequent cleavage in the sink tissues is the first step for utilization of the photoassimilate in various metabolic pathways. Sucrose synthase (Sus) plays a major role(s) in sucrose metabolism in a number of different growth processes within a variety of sink tissues. Sus catalyzes a reaction of sucrose and UDP to form fructose and UDPG, the latter being a precursor of complex saccharide biosynthesis. Sus is also proposed to supply UDP-glucose for cellulose synthesis in the cell wall, and in cotton fiber which is supported by experimental evidence from antisense suppression of the enzyme. In addition to these major roles in sink tissue metabolism, Sus gene expression has also been reported to be induced in response to environmental stresses such as hypoxia and cold. Further roles for Sus were proposed in other important metabolic processes including nitrogen fixation in legume nodules and phloem loading and/or unloading. Specially, rice sucrose synthase 3(RSUS3) has its own role in sucrose metabolism. First, Tatsuro Hirose et al and Wang et al suggest that SUS3 play a catalyzed reaction when the RSUS1 which is rich in the phloem and aleurone layers of the seeds, transport sugar into the endosperm cells. Second, RSUS3 is expressed predominantly in rice seed endosperm and is thought to play an important role in starch filling during the milky stage of rice seed ripening . Third, SUS3 and SUS4 were predominantly expressed in the caryopsis, indicating potential roles in carbon allocation within the filling grain and participated in the cleavage of sucrose, taken up by aleurone, thus providing the precursors for starch synthesis.

Expression

Wang et al used the mono-specific antibodies for three RSuS isoforms and found differentially and developmentally regulated expression of three rice sucroce synthase genes. The expression of RSuS3 could only be detected in the seeds in etiolated seedlings.

picture 4. Distribution of RSuS isozymes in various rice tissues (from reference ).

However, researchers found temporal expression of RSus3 genes in developing seeds. RSuS3 was barely detectable before 3 DAP and reached a plateau from 6 to 12 DAP, or the milky stage in which the starch filling in the endosperm was the most active.

picture 5. Temporal expression of RSuS in seeds at various maturation stages (from reference ).

Tatsuro Hirose et al used Real-time RT-PCR to determine the expression profile for each member of the Sus gene family in various tissues of rice and found tissue-specific expression of each member of the Sus gene family. The transcript of SUS3 was most abundant in either the panicles at the grain filling stage of development or dry seeds respectively, and was absent from or expressed only at very low levels in the other tissues examined.

picture 6A. The transcript levels of the SUS genes in various rice tissues (from reference ).

Furthermore, to investigate the response of the SUS genes to submergence, their transcript levels were determined in the shoots of seedlings, germinated under submerged conditions, during a developmental time-course from 3 to 7 days after imbibition (DAI). The SUS3 transcript was not detectable in both control and submerged samples.

picture 9.Sus activity and transcript levels of four of the rice SUS genes in germinating shoots in response to submergence ).

Nucleotide Polymorphisms

Nucleotide changes and indels at the RSUS3 locus were identified, and the results are summarized in picture 10.

picture10. Summary of the frequency of polymorphisms (from reference ).

Puji Lestari analyzed the full sequence of RSUS3 from 43 rice varieties consisting of 13 indica varieties, 22 japonica varieties, and 8 wild rice accessions( Oryza rufipogon) to examine the distribution of DNA polymorphisms, revealed allelic diversity at the RSUS3 locus. Sequence polymorphisms were detected across the length of 7733 bp, which covers a 1652 bp upstream region, a 2815 bp coding region, a 2724 bp noncoding region, and a 542 bp downstream region. No triallelic SNPs were found in any of the defined regions. The frequency of SNPs/indels was highest in the promoter region. The 3’ NTR contained abundant nucleotide and length polymorphisms (frequency of total variants 50.041). However, the overall indel frequency in the transcribed region was higher than the nucleotide substitution frequency in the region. The SNP frequency in the coding region was less than the average of SNP frequency in the entire transcribed region; one SNP occurred every 216.5 bp in the coding region. The frequency of nucleotide substitutions was about 1.6 times higher in the noncoding region than in the coding region, and both nucleotide changes and indels were more frequent in the noncoding region than in the coding region. The differences in the distribution of the differences in the lengths of the indels in all regions varied in size from 1 to 32 bp, with an average indel length of 2.87 bp. The distribution of SNP and indel sites was not significantly different (when degrees of freedom =2, SNPs χ2=0.228; indels χ2=0.377) across the entire region excluding intron (5’ NTR-transcript-3’ NTR).

Allele Distribution

Puji Lestari adopted Tajima’s D test and Fu and Li’s D* and F* tests to evaluate the allele distribution in the germplasm used in this study and assess the neutrality of the mutations. The frequency spectrum of polymorphic sites for the total length was skewed toward a deficit of low-frequency alleles relative to expectations based on a positive outcome by Tajima’s D test (0.923). The Tajima’s D value for the total region of RSUS3 excluding intron was lower than that for the entire length. Separate Tajima’s D tests for each region (upstream, coding, and noncoding region) revealed positive and nonsignificant departures from the neutral expectation, with the exception of the 3’ downstream NTR, which had a negative Tajima’s D value (D = -0.326). Using the coalescent process to test the neutrality of the mutations in the entire gene sequence, similar positive values were obtained, but significant deviation from the neutral expectation (P <0.02) occurred with the Fu and Li D* (1.959) and F* (1.894) tests. A summary of this neutrality test is presented in picture 11.

picture11. Nucleotide diversity and divergence in each region of theRSUS3gene (from reference ).

Haplotype Diversity

Some researchers predicted initially the number of haplotypes of RSUS3 using the coalescent theory. The predicted haplotype numbers for each functional part of the promoter, transcript, and downstream region were 17, 12, and 12, respectively. The highest haplotype diversity (Hd: 0.866) was observed in the promoter region, and the lowest Hd (0.828) was observed in the downstream region. Puji Lestari analyzed the entire region excluding intron revealed that the nucleotide diversity ranged from 1.645 to 1.801, and the estimated haplotype number was from 10 to 22. Finally, using bootstrap analysis, the genealogy of the sequences containing 11 major highly differentiated haplotypes groups across the region of 5’ NTR-transcript-3’ NTR was successfully assembled. They constructed a neighbor joining tree to illustrate the phylogenetic branching order between the 5’ NTR transcript-3’ NTR and to elucidate the evolutionary history(picture 12).

picture 12. Neighbor joining tree representing the RSUS3 haplotype relationships based on the entire region excluding intron (upstream, transcript, and 3' downstream NTR sequence) (from reference ).

Recombination

Puji Lestari used the algorithm of Hudson and Kaplan to determine that at least 11 recombination events were responsible for the polymorphism pattern identified in the RSUS3 gene. The recombinations were detected in the informative sites of the 3 regions: a minimum of 3 recombinations in the 5’ NTR (-1639 to -1630, -1594 to -1588, and -679 to -600), 4 in the transcribed region (1072–2734, 2734–3305, 4117–4148, and 4148–4572), 1 in the position between the transcribed region and the downstream region (4572–5627), and 3 in the 3’ NTR (5627–5923, 6041–6050, and 6050–6055). A total of 48 polymorphic sites in the entire region without intron were analyzed for evidence of recombination.

Evolution

Sequence analysis revealed that RSUS2 and RSUS3 may have evolved from the same ancestor after the divergence of RSUS1.

Labs working on this gene

• National Agricultural Research Center,1-2-1 Inada, Joetsu, Niigata 943-0193, Japan
• CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
• Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan 106, R.O.C.
• Department of Agronomy, National Taiwan University, Taipei, Taiwan 106, R.O.C.
• The Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
• The National Academy of Agricultural Sciences, Rural Development Administration, Suwon, Korea
• The Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor, Indonesia