Henrik H. Albert

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3× draft genome sequence of ‘SunUp’ papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica’s distinguishing morpho-physiological, medicinal and nutritional properties.

Comparative expression analysis of two sugarcane polyubiquitin promoters and flanking sequences in transgenic plants

GUS (uidA) reporter gene expression for two sugarcane polyubiquitin promoters, ubi4 and ubi9, was compared to expression from the maize Ubi-1 promoter in stable transgenic rice (only ubi9) and sugarcane (ubi4 and ubi9). Ubi9 drove high-level GUS expression, comparable to the maize Ubi-1 promoter, in both callus and regenerated plants of rice transformed by Agrobacterium. This high level expression was inherited in R1 plants. Expression from ubi4 and ubi9 was quite high in sugarcane callus transformed via particle bombardment. Expression dropped to very low or undetectable levels in the resulting plants; this drop in expression resulted from PTGS. PTGS in regenerated sugarcane plants also occurred with the maize Ubi-1 promoter. In sugarcane callus, ubi4 was HS inducible, but ubi9 was not. This physiological difference corresponds to a MITE insertion that is present in the putative HSEs of ubi9 but not present in ubi4.

Metabolic engineering of invertase activities in different subcellular compartments affects sucrose accumulation in sugarcane cells

Transgenic sugarcane (Saccharum officinarum L.) lines were created to express altered invertase isoform activity to elucidate the role(s) of invertase in the sucrose accumulation process. A sugarcane soluble acid invertase cDNA (SCINVm, AF062734) in the antisense orientation was used to decrease invertase activity. The Saccharomyces cerevisiae invertase gene (SUC2), fused with appropriate targeting elements, was used to increase invertase activity in the apoplast, cytoplasm and vacuole. A callus/liquid culture system was established to evaluate change in invertase activity and sugar concentration in the transgenic lines. Increased invertase activity in the apoplast led to rapid hydrolysis of sucrose and rapid increase of hexose in the medium. The cellular hexose content increased dramatically and the sucrose level decreased. Cells with higher cytoplasmic invertase activity did not show a significant change in the sugar composition in the medium, but did significantly reduce the sucrose content in the cells. Transformation with the sugarcane antisense acid invertase gene produced a cell line with moderate inhibition of soluble acid invertase activity and a 2-fold increase in sucrose accumulation. Overall, intracellular and extracellular sugar composition was very sensitive to the change in invertase activities. Lowering acid invertase activity increased sucrose accumulation.

Production of biologically active GM-CSF in sugarcane: a secure biofactory

Over 300 transgenic sugarcane plants representing approx. 200 independent lines producing the human cytokine granulocyte macrophage colony stimulating factor (GM-CSF) were analyzed for recombinant protein accumulation and activity levels. Expression constructs differed in use of the maize polyubiquitin 1, Mubi-1, or the sugarcane polyubiquitin 9, SCubi9, promoters; presence or absence of a C-terminal HDEL tag for ER retention; and presence or absence of a 6X Histidine tag for metal ion affinity purification. Accumulation of GM-CSF protein ranged from undetectable to 0.02 of total soluble protein. No significant difference was observed between the two promoters; however, the ER retention tag was required for higher accumulation levels. Human bone marrow cells (TF-1), which require GM-CSF for cell division, proliferated when growth media was supplemented with transgenic sugarcane extracts. Comparison to purified commercially produced GM-CSF indicated the sugarcane-produced protein had essentially identical activity levels. In a 14-month field trial, accumulation levels remained stable. This is the first report of field production of GM-CSF. During the field trial, no flowering of the trial plants occurred; no pollen or seed was produced. Drying, burning, and burial of the test plants effectively blocked possible routes for the transgenic sugarcane to enter the environment or food supply. Sugarcane may provide a highly secure system for biofactory production of pharmaceutical proteins.

The P0 gene of Sugarcane yellow leaf virus encodes an RNA silencing suppressor with unique activities.

The Sugarcane yellow leaf virus (SCYLV) P0, a member of the highly heterologous proteins of poleroviruses, is a suppressor of posttranscriptional gene silencing (PTGS) and has additional activities not seen in other P0 proteins. The P0 protein in previously tested poleroviruses (Beet western yellows virus and Cucurbit aphid-borne yellows virus), suppresses local, but not systemic, PTGS induced by both sense GFP and inverted repeat GF using its F-box-like domain to mediate destabilization of the Argonaute1 protein. We now report that the SCYLV P0 protein not only suppressed local PTGS induced by sense GFP and inverted repeat GF in Nicotiana benthamiana, but also triggered a dosage dependent cell death phenotype in infiltrated leaves and suppressed systemic sense GFP-PTGS. Deletion of the first 15 N-terminal amino acid residues of SCYLV P0 abolished suppression of both local and systemic PTGS and the induction of cell death. In contrast, only systemic PTGS and cell death were lost when the 15 C-terminal amino acid residues were deleted. We conclude that the 15 C-terminal amino acid residue region of SCYLV P0 is necessary for suppressing systemic PTGS and inducing cell death, but is not required for suppression of local PTGS.

Effective selection of transgenic papaya plants with the PMI/Man selection system.

The selectable marker gene phospho-mannose isomerase (pmi), which encodes the enzyme phospho-mannose isomerase (PMI) to enable selection of transformed cell lines on media containing mannose (Man), was evaluated for genetic transformation of papaya (Carica papaya L.). We found that papaya embryogenic calli have little or no PMI activity and cannot utilize Man as a carbon source; however, when calli were transformed with a pmi gene, the PMI activity was greatly increased and they could utilize Man as efficiently as sucrose. Plants regenerated from selected callus lines also exhibited PMI activity but at a lower specific activity level. Our transformation efficiency with Man selection was higher than that reported using antibiotic selection or with a visual marker. For papaya, the PMI/Man selection system for producing transgenic plants is a highly efficient addition to previously published methods for selection and may facilitate the stacking of multiple transgenes of interest. Additionally, since the PMI/Man selection system does not involve antibiotic or herbicide resistance genes, its use might reduce environmental concerns about the potential flow of those genes into related plant populations.

Differential expression of soluble acid invertase genes in the shoots of high-sucrose and low-sucrose species of Saccharum and their hybrids

The hydrolytic activity of soluble acid invertase (SAI) is strongly correlated to sucrose accumulation in sugarcane (Saccharum spp.). Plants exhibiting SAI activity above a low threshold level do not accumulate high concentrations of sucrose. The present work investigates the basis for the difference in SAI activity observed between high- and low-sucrose-accumulating sugarcane lines. SAI-encoding cDNAs were isolated from two high- and one low-sucrose lines. All of these cDNAs were highly similar, with deduced proteins at least 98% identical. Expression of SAI in the stem of sugarcane was developmentally regulated, with relatively larger pools of SAI protein and mRNA in the apex and young internodes, which declined rapidly in the maturing internodes where sucroseaccumulation occurs. This developmental pattern, while qualitatively similar, was quantitatively quite different between low- and high-sucrose lines. SAI protein and mRNA pools started substantially higher, declined later, and stabilized at a significantly higher level in a low-sucrose line than in a high-sucrose line. These data indicate that differences in SAI activity between high- and low-sucrose sugarcane lines are due, at least in part, to differences inthe level of expression of essentially identical SAI genes.

Cloning and characterization of a FLORICAULA/LEAFY ortholog, PFL, in polygamous papaya.

ABSTRACTThe homologous genes FLORICAULA (FLO) in Antirrhinum and LEAFY (LFY) in Arabidopsis are known to regulate the initiation of flowering in these two distantly related plant species. These genes are necessary also for the expression of downstream genes that control floral organ identity. We used Arabidopsis LFY cDNA as a probe to clone and sequence a papaya ortholog of LFY, PFL. It encodes a protein that shares 61% identity with the Arabidopsis LFY gene and 71% identity with the LFY homologs of the two woody tree species: California sycamore (Platanus racemosa) and black cottonwood (Populus trichocarpa). Despite the high sequence similarity within two conserved regions, the N-terminal proline-rich motif in papaya PFL differs from other members in the family. This difference may not affect the gene function of papaya PFL, since an equally divergent but a functional LFY ortholog NEEDLY of Pinus radiata has been reported. Genomic and BAC Southern analyses indicated that there is only one copy of PFL in the papaya genome. In situ hybridization experiments demonstrated that PFL is expressed at a relatively low level in leaf primordia, but it is expressed at a high level in the floral meristem. Quantitative PCR analyses revealed that PFL was expressed in flower buds of all three sex types - male, female, and hermaphrodite with marginal difference between hermaphrodite and unisexual flowers. These data suggest that PFL may play a similar role as LFY in flower development and has limited effect on sex differentiation in papaya.

Differential expression of sugarcane polyubiquitin genes and isolation of promoters from two highly-expressed members of the gene family

Summary To identify potential strong constitutive promoters, accumulation of polyubiquitin mRNA in sugarcane ( Saccharum hybrid) was studied using gene-specific probes from five sugarcane polyubiquitin cDNA clones. Based on comparisons of 3′ untranslated regions, these cDNAs can be grouped into four sub-groups within the sugarcane polyubiquitin gene family. RNA gel blot experiments indicated that these sub-groups differ substantially in constitutive expression levels and response to heat shock. Reverse northern experiments confirmed the relative magnitudes of constitutive expression in young leaves. One sub-group, homologous to cDNAs scubi241 and scubi511, was found to have the highest level of constitutive expression and to be little affected by heat shock. Genomic clones belonging to this sub-group were isolated; two of these clones, ubi4 and ubi9, were found to differ in the number of protein coding repeats but were highly similar in overall structure and in the sequence of DNA flanking the transcribed region. Both genes contain a single large intron located immediately upstream of the translation start codon. Transient expression experiments showed that the cloned promoters are sufficient to drive high levels of GUS expression in sugarcane suspension cells and in tobacco leaves.

Cre- lox Directed Integration of Transgenes into the Tobacco Genome

Several site-specific recombination systems have been tested for genome manipulations in plants [17]. One particular application is to direct the insertion of DNA into recombination sites previously placed into the genome [2]. Because it is a commonly held belief that expression variation results from “position effects” (the random chromosome locations of transgenes), integrating DNA into a defined chromosome location is thought to reduce transgene expression variability among independent transformants. There is recent indication that this “position effect” does not account for all of the variability of transgene expression [16]. However, site-specific DNA integration remains an attractive transformation tool for additional reasons: It can produce transgenic plants that predominantly harbor single copy and precise molecules, i.e., molecules without the rearrangements and truncations frequently seen with other transformation systems [1]. To have single copy insertions may by itself eliminate one of the factors most frequently linked to multicopy associated transgene silencing [13, 18].