Structural analysis of the chloroplastic and cytoplasmic aldolase-encoding genes implicated the occurrence of multiple loci in rice

Characterization of FBA genes in potato (Solanum tuberosum L.) and expression patterns in response to light spectrum and abiotic stress

Fructose-1, 6-bisphosphate aldolase (FBA) plays vital roles in plant growth, development, and response to abiotic stress. However, genome-wide identification and structural characterization of the potato (Solanum tuberosum L.) FBA gene family has not been systematically analyzed. In this study, we identified nine StFBA gene members in potato, with six StFBA genes localized in the chloroplast and three in the cytoplasm. The analysis of gene structures, protein structures, and phylogenetic relationships indicated that StFBA genes were divided into Class I and II, which exhibited significant differences in structure and function. Synteny analysis revealed that segmental duplication events promoted the expansion of the StFBA gene family. Promoter analysis showed that most StFBA genes contained cis-regulatory elements associated with light and stress responses. Expression analysis showed that StFBA3, StFBA8, and StFBA9 showing significantly higher expression levels in leaf, stolon, and tuber under blue light, indicating that these genes may improve photosynthesis and play an important function in regulating the induction and expansion of microtubers. Expression levels of the StFBA genes were influenced by drought and salt stress, indicating that they played important roles in abiotic stress. This work offers a theoretical foundation for in-depth understanding of the evolution and function of StFBA genes, as well as providing the basis for the genetic improvement of potatoes.

Characterization of Glycolytic Pathway Genes Using RNA-Seq in Developing Kernels of Eucommia ulmoides

Eucommia ulmoides Oliver, the only member of the Eucommiaceae family, is a rare and valuable tree used to produce a highly valued traditional Chinese medicine and contains α-linolenic acid (ALA) up to 60% of the total fatty acids in the kernels (embryos). Glycolysis provides both cellular energy and the intermediates for other biosynthetic processes. However, nothing was known about the molecular basis of the glycolytic pathway in E. ulmoides kernels. The purposes of this study were to identify novel genes of E. ulmoides related to glycolytic metabolism and to analyze the expression patterns of selected genes in the kernels. Transcriptome sequencing based on the Illumina platform generated 96,469 unigenes in four cDNA libraries constructed using RNAs from 70 and 160 days after flowering kernels of both low- and high-ALA varieties. We identified and characterized the digital expression of 120 unigenes coding for 24 protein families involved in kernel glycolytic pathway. The expression levels of glycolytic genes were generally higher in younger kernels than in more mature kernels. Importantly, several unigenes from kernels of the high-ALA variety were expressed more than those from the low-ALA variety. The expression of 10 unigenes encoding key enzymes in the glycolytic pathway was validated by qPCR using RNAs from six kernel stages of each variety. The qPCR data were well consistent with their digital expression in transcriptomic analyses. This study identified a comprehensive set of genes for glycolytic metabolism and suggests that several glycolytic genes may play key roles in ALA accumulation in the kernels of E. ulmoides.

Two cytosolic aldolases show different expression patterns during shoot elongation in Moso bamboo, Phyllostachys pubescens Mazel

In fast-growing Moso bamboo (Phyllostachys pubescens Mazel), cytosolic fructose 1,6-bisphosphate aldolase (aldolase; EC 4.2.2.13) was more highly active in elongating tissues than in tissues that had already finished elongating. It is well known that the removal of the culm sheath prevents bamboo from elongating. When the sheath was removed from the culm, the aldolase activity was gradually reduced over time. Two isozyme genes for aldolase, PpAldC1 and PpAldC2, were cloned from the elongating tissues of Moso bamboo. Gene expression analysis using a semi-quantitative reverse transcriptase-polymerase chain reaction revealed that PpAldC1 was highly expressed in elongating tissues but was hardly detected in elongated internodes, while PpAldC2 seemed to be expressed constitutively in both elongating and elongated tissues. Promoter analysis revealed that the expression of PpAldC1 was induced by gibberellin. These results indicated that the two genes for cytosolic aldolase in Moso bamboo showed different expression patterns and that one of them was involved in shoot elongation.

Identification and characterization of fructose 1,6-bisphosphate aldolase genes in Arabidopsis reveal a gene family with diverse responses to abiotic stresses

Fructose 1,6-biphosphate aldolase (FBA) is a key enzyme in plants, which is involved not only in glycolysis and gluconeogenesis in the cytoplasm, but also in the Calvin cycle in plastids. Research on FBAs in various organisms has been reported, but there is none on FBAs in Arabidopsis at the molecular level. In the current study, eight FBA family genes (AtFBA1-8) were identified and analyzed in Arabidopsis thaliana. These genes have a highly conserved aldolase-type TIM barrel domain and a C-terminal peptide, but variable N-terminal peptides. Based on the phylogenetic analysis of FBA protein sequences from Arabidopsis and other plant species, AtFBA family was classified into two subfamilies, including three members (AtFBA1-3) with high similarities to FBAs occurring at plastid, and five (AtFBA4-8) with high similarities to FBAs localized in the cytoplasm. By confocal microscopy analysis with GFP fusion protein, AtFBA3 and AtFBA4 as well as AtFBA6 were observed to be localized in the plastid and cytoplasm, respectively. At least two duplicated gene pairs of AtFBA1 and AtFBA2, as well as AtFBA4 and AtFBA8 were found. Transcript level analysis of AtFBA genes in various tissues revealed the unique and overlapping expression patterns of plastid and cytosol AtFBA genes, suggesting that these genes may function at different stages of plant growth and development. Interestingly, AtFBA1, AtFBA2, AtFBA5 and AtFBA7 showed undetectable expression in roots. The expression patterns of AtFBA genes under different stress conditions suggested that all the members showed different expression patterns in response to stresses, including ABA, NaCl, Cd, abnormal temperature and drought, and, except for AtFBA3, most of the AtFBA genes were significantly responsive to drought stress in roots. Moreover, AtFBA1, AtFBA2, AtFBA5, AtFBA7 and AtFBA8 were induced by at least one of three sugars (sucrose, glucose and fructose) after 24h of treatment. Further functional analyses indicated important clues of AtFBA2, AtFBA6 and AtFBA8 in plant growth, stress responses and development, respectively. Thus these results provide additional knowledge on AtFBA families and their roles.

Continuously coupled transcription-translation system for the production of rice cytoplasmic aldolase

A continuously coupled cell-free transcription-translation system was developed for the production of rice cytoplasmic aldolase, an enzyme involved in both glycolytic and gluconeogenic pathways in eukaryotic cells. The system works with a continuous flow of feeding solution containing nucleoside triphosphates and amino acids into a 1-mL reactor containing wheat-germ extract, plasmid DNA, and transcription enzyme, and continuous removal of translation product through an ultrafiltration membrane fitted in the reactor. Addition of free nucleotide primer, m(7)G(5')ppp(5')G, to this reactor was necessary for efficient transcription, thus producing biologically active mRNA for translation. The rate of aldolase synthesis was constant during the continuous translation reaction. It was observed that from 3 h onward only aldolase was synthesized by the system. After 30 h, the total amount of protein synthesized reached 205.6 microg, which is comparable with the amount synthesized (255.6 microg) in the translation system only where separately prepared capped mRNAs were added to the reactor for translation. Autoradiogram and Western blot analyses of the translated product showed a distinct band corresponding to the calculated molecular weight of the protein. These results have shown the establishment of a continuously coupled eukaryotic transcription-translation system for the expression of genes from eukaryotic cells.

Cloning of a NaCl-induced fructose-1, 6-diphosphate aldolase cDNA from Dunaliella salina and its expression in tobacco

Using Rapid Amplification of cDNA ends (RACE) technique, the full-length cDNA encoding a NaCl-induced fructose-1, 6-diphosphate aldolase (DsALDP) was obtained. It was shown that the DsALDP had a relatively high homology (66%-73%) to chloroplast fructose-1, 6-diphosphate aldolase (AldP) in many plants according to their amino acid sequences. The phylogenetic analysis further confirmed that AldP in alga is the nearest to DsALDP. As to its expression pattern, DsALDP was de novo synthesized by NaCl induction. Its expression level was significantly changed with inducing time. After the selected DsALDP cDNA subcloned into a binary vector pBI121, the new construct was introduced into tobacco by Agrobacterium tumefaciens. The results of Southern blot and RT-PCR analysis of four transgenic T1 plants indicated that DsALDP was integrated into genome of these transgenic plants and effectively expressed. Aldolase activities have been detected in T1-1, T1-2 and T1-3 plants by bioassay under 100-200 mmol/L NaCl. It was also observed that proline contents in them were differentially increased.

Differential expression of plastidic aldolase genes in Nicotiana plants under salt stress

Two homologous genes of plastidic fructose-1,6-bisphosphate aldolase (AldP) isozymes were isolated from green leaves of a salt stress-tolerant Nicotiana species, Nicotiana paniculata, by differential screening. The products of the corresponding genes, NpAldP1 and NpAldP2, were 91% identical to each other and 70-85% identical to the other known plant plastidic aldolases. Although these two genes showed similar organ-specific expression and daily cycles, their responses to salt stress differed: mRNA accumulation of NpAldP2 increased, but that of NpAldP1 slightly decreased. The mRNA accumulations of their counterparts of two other Nicotiana species, NeAldP1 and NeAldP2 (Nicotiana excelsior), and NaAldP1 and NaAldP2 (Nicotiana arentsii) were studied under the same stress condition. N. arentsii conserved accumulation profiles similar to N. paniculata, but N. excelsior did not. In N. excelsior, accumulation of NeAldP1 decreased to 50% of the control after stress and gradually recovered thereafter, whereas accumulation of NeAldP2 temporarily decreased and reached 250% of the control by the third day of stress. Southern blot analysis indicated that NpAldP1, NpAldP2, NaAldP1, and NaAldP2 include one or two closely related genes and NeAldP1 and NeAldP2 several.

Protein changes in response to progressive water deficit in maize . Quantitative variation and polypeptide identification

Three-week-old plants of two unrelated lines of maize (Zea mays L.) and their hybrid were submitted to progressive water stress for 10 d. Changes induced in leaf proteins were studied by two-dimensional electrophoresis and quantitatively analyzed using image analysis. Seventy-eight proteins out of a total of 413 showed a significant quantitative variation (increase or decrease), with 38 of them exhibiting a different expression in the two genotypes. Eleven proteins that increased by a factor of 1.3 to 5 in stressed plants and 8 proteins detected only in stressed plants were selected for internal amino acid microsequencing, and by similarity search 16 were found to be closely related to previously reported proteins. In addition to proteins already known to be involved in the response to water stress (e.g. RAB17 [Responsive to ABA]), several enzymes involved in basic metabolic cellular pathways such as glycolysis and the Krebs cycle (e.g. enolase and triose phosphate isomerase) were identified, as well as several others, including caffeate O-methyltransferase, the induction of which could be related to lignification.

A moderate decrease of plastid aldolase activity inhibits photosynthesis, alters the levels of sugars and starch, and inhibits growth of potato plants

Antisense expression of a full length cDNA encoding plastid aldolase led to decreased expression of aldolase at the transcript and protein level in several 'antisense' potato transformants. To quantify the inhibition, activity was compared in corresponding leaves down a plant and in plants of different ages. Aldolase activity was decreased by 32-43%, 56-71%, 79-83% and 91-97% in A-70, A-3, A-51 and A-2. Separation on a Q-Sepharose-FF column showed the decrease was due to inhibition of plastid aldolase. The transformants showed a small increase of Rubisco activity, a small decrease of phosphoribulokinase activity, and larger but subproportional decreases of sedoheptulose-1,7-biphosphatase and plastid fructose-1,6-bisphosphatase activity. Ambient photosynthesis was inhibited by 10%, 40%, 66% and 85% in A-70, A-3, A-51 and A-2. The transformants contained increased triose phosphates, and very low ribulose-1,5-bisphosphate and glycerate-3-phosphate. Chlorophyll fluorescence indicated that photosystem II was more reduced and thylakoid energization was increased. Starch synthesis was decreased by 16% and 36% in A-70 and A-3, whereas sucrose synthesis was less strongly inhibited. Plant growth was not significantly altered in A-70, was decreased by 41% in A-3, and was severely inhibited in plants with under 20% of wild-type aldolase activity. Although plastid aldolase catalyses a readily reversible reaction, possesses no known regulatory properties, and would appear irrelevant for the control of metabolism and growth, small changes in its activity have marked consequences for photosynthesis, carbon partitioning and growth.

Caenorhabditis elegans has two isozymic forms, CE-1 and CE-2, of fructose-1,6-bisphosphate aldolase which are encoded by different genes

Two distinct types of cDNAs for fructose-1,6-bisphosphate (FBP) aldolase, Ce-1 and Ce-2, have been isolated from nematode Caenorhabditis elegans, and the respective recombinant aldolase isozymes, CE-1 and CE-2, have been purified and characterized. The Ce-1 and Ce-2 are 1282 and 1248 bp in total length, respectively, and both have an open reading frame of 1098 bp, which encodes 366 amino acid residues. The entire amino acid sequences deduced from Ce-1 and Ce-2 show a high degree of identity to one another and to those of vertebrate and invertebrate aldolases. The highest sequence diversity was found in the carboxyl-terminal region that corresponds to one of the isozyme group-specific sequences of vertebrate aldolase isozymes that play a role in determining isozyme-specific functions. Southern blot analysis suggests that CE-1 and CE-2 are encoded by different genes. Concerning general or kinetic properties, CE-2 is quite different from CE-1. CE-1 exhibits unique characteristics which are not identical to any aldolase isozymes previously reported, whereas CE-2 is similar to vertebrate aldolase C. These results suggest that CE-2 might preserve the properties of a progenitor aldolase with a moderate preference for FBP over fructose 1-phosphate (F1P) as a substrate, whereas CE-1 evolved to act as an intrinsic enzyme that exhibits a much broader substrate specificity than dose CE-2.

Genomic structure of the rice aldolase isozyme C-1 gene and its regulation through a Ca 2+ -mediated protein kinase-phosphatase pathway

Complementary and genomic DNA clones coding for aldolase C-1, the fourth-type isozyme of aldolase in rice Oryza sativa L., have been characterized. The organization of the gene is quite similar to those encoding rice aldolase C-a and a maize cytoplasmic-type aldolase, in that introns are located in the same position. Amino acid sequences are highly conserved among cytoplasmic aldolases in plants. Expression of the gene in rice callus is activated by a protein phosphatase inhibitor okadaic acid, and is inhibited in the presence of thapsigargin, a reagent which increases calcium influx into the cytoplasm. The inhibition is rescued by the simultaneous addition of protein kinase inhibitor H-7. Thus, it is suggested that expression of the aldolase C-1 gene is regulated through a signal transduction pathway involving a Ca 2+ -mediated protein kinase-protein phosphatase system.

The promoter from the rice nuclear gene encoding chloroplast aldolase confers mesophyll-specific and light-regulated expression in transgenic tobacco

The rice genome contains at least four separate loci that encode aldolase isozymes. Among these, the aldolase P (AldP) gene, a nuclear gene coding for chloroplast aldolase, is expressed predominantly in the leaf blade mesophyll cells in rice. To dissect promoter elements that regulate such tissue- or cell type-specific expression, we constructed various AldP promoter-beta-glucuronidase (GUS) fusion genes and transferred them into Nicotiana tabacum (tobacco) plants. Analysis of GUS activities in the transgenic tobacco revealed the presence of at least two elements within 2.0 kb AldP promoter region. One is located within the segment from position -2.0 kb to -1.2 kb and acts as a negative element. The other is a positive element located between -1.2 kb and -0.31 kb that confers developmentally regulated, mesophyll cell-specific expression. In addition, the 1.2 kb rice promoter segment flanking the transcription start site contains an element(s) that serves as target for light induction in tobacco. The results suggest that the AldP gene promoter of rice, a monocot promoter, can function in an essentially physiological manner in the dicot tobacco plant.

The plastid aldolase gene from Chlamydomonas reinhardtii: intron/exon organization, evolution, and promoter structure

Genomic clones encoding the plastidic fructose-1,6-bisphosphate aldolase of Chlamydomonas reinhardtii were isolated and sequenced. The gene contains three introns which are located within the coding sequence for the mature protein. No introns are located within or near the sequence encoding the transit-peptide, in contrast to the genes for plastidic aldolases of higher plants. Neither the number nor the positions of the three introns of the C. reinhardtii aldolase gene are conserved in the plastidic or cytosolic aldolase genes of higher plants and animals. The 5' border sequences of introns in the aldolase gene of C. reinhardtii exhibit the conserved plant consensus sequence. The 3' acceptor splice sites for introns 1 and 3 show much less similarity to the eukaryotic consensus sequences than do those of intron 2. The plastidic aldolase gene has two tandemly repeated CAAT box motifs in the promoter region. Genomic Southern blots indicate that the gene is encoded by a single locus in the C. reinhardtii genome.