Edson L. Kemper

The libraries that made SUCEST

A large-scale sequencing of sugarcane expressed sequence tags (ESTs) was carried out as a first step in depicting the genome of this important tropical crop. Twenty-six unidirectional cDNA libraries were constructed from a variety of tissues sampled from thirteen different sugarcane cultivars. A total of 291,689 cDNA clones were sequenced in their 5x92 and 3x92end regions. After trimming low-quality sequences and removing vector and ribosomal RNA sequences, 237,954 ESTs potentially derived from protein-encoding messenger RNA (mRNA) remained. The average insert size in all libraries was estimated to be 1,250bp with the insert length varying from 500 to 5,000 bp. Clustering the 237,954 sugarcane ESTs resulted in 43,141clusters, from which 38% had no matches with existing sequences in the public databases. Around 53% of the clusters were formed by ESTs expressed in at least two libraries while 47% of the clusters are formed by ESTs expressed in only one library. A global analysis of the ESTs indicated that around 33% contain cDNA clones with full-length insert.

Regulation of lysine catabolism in higher plants

Lysine is an essential amino acid for mammals but its concentration in cereals, one of our main food sources, is low. Research over the past 40 years has unraveled many biochemical and molecular details of the aspartic acid pathway, which is the main route of lysine biosynthesis in plants. However, genetic manipulation of this pathway has not been successful at producing high-lysine seeds. This is because lysine, instead of being accumulated, is degraded via the saccharopine pathway. Recent work has increased our knowledge of this pathway, including both the enzymes involved and their regulation.

The mitochondrial genome of the primary screwworm fly Cochliomyia hominivorax (Diptera: Calliphoridae)

The complete sequence of the mitochondrial genome of the screwworm Cochliomyia hominivorax was determined. This genome is 16 022 bp in size and corresponds to a typical Brachycera mtDNA. A Serine start codon for COI and incomplete termination codons for COII, NADH 5 and NADH 4 genes were described. The nucleotide composition of C. hominivorax mtDNA is 77% AT‐rich, reflected in the predominance of AT‐rich codons in protein‐coding genes. Non‐optimal codon usage was commonly observed in C. hominivorax mitochondrial genes. Phylogenetic analysis distributed the Acalypterate species as a monophyletic group and assembled the C. hominivorax (Calyptratae) and the Acalyptratae in a typical Brachycera cluster. The identification of diagnostic restriction sites on the sequenced mitochondrial genome and the correlation with previous RFLP analysis are discussed.

The role of opaque2 in the control of lysine-degrading activities in developing maize endosperm.

We have isolated a cDNA clone, designated ZLKRSDH, encoding the bifunctional enzyme lysine–ketoglutarate reductase/saccharopine dehydrogenase (LKR/SDH) from maize. The predicted polypeptide has an N-terminal LKR domain and a C-terminal SDH domain that are similar to the yeast LYS1 and LYS9 monofunctional proteins, respectively. The maize LKR/SDH protein is located in the cytoplasm of subaleurone endosperm cell layers. Transcripts and polypeptides as well as enzyme activities showed an upregulation and downregulation during endosperm development. The developmental expression of ZLKRSDH was examined in normal and opaque2 seeds. In the mutant endosperm, mRNA levels were reduced by >90%, with concomitant reductions in polypeptide levels and LKR/SDH activity. These results suggest that lysine levels in the endosperm are likely to be controlled at the transcriptional level by the Opaque2 transcription factor.

Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome

Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.

Effect of microprojectile bombardment parameters and osmotic treatment on particle penetration and tissue damage in transiently transformed cultured immature maize (Zea mays L.) embryos

Abstract Immature maize ( Zea mays L.) embryos of the tropical inbred line Cat-100-6, plated in callus induction medium for short periods, were used to study the effect of microprojectile bombardment parameters and osmotic treatment on the transformation of embryogenic competent cells. Somatic embryogenesis in this material arose from sub-epidermal cell clusters located at the third or deeper cell layer. Experiments were carried out focusing on the transformation of these cell clusters following microprojectile bombardment. Physical conditions such as particle delivering method, particle size, helium pressure and target distance were analyzed in factorial experiments. The best condition which permitted the transformation of embryogenic cell clusters at relatively high frequency was found to cause deleterious tissue damage because of the bombardment at high pressure and short target distance. Tissue damage as successfully prevented by the addition of mannitol in the culture medium before and after bombardment.

Development of Transgenic Sugarcane Resistant to Sugarcane Borer

Sugarcane borer (Diatraea saccharalis) is a major pest of sugarcane (Saccharum spp. hybrids), across the Americas. The insect is partially controlled by biological and chemical means, but still causes significant economic losses to sugarcane growers and processors. Proteins derived from Bacillus thuringiensis, Bt proteins, have been used to control sugarcane borer in maize (Zea mays) for the past decade. In sugarcane, the expression of individual Bt proteins has been reported several times. However practical use of Bt proteins requires their use as part of an Integrated Pest Management (IPM) system that includes the delivery of high doses of protein and the use of a refuge to slow the evolution of insect resistance to the protein. Here we demonstrate the feasibility of using Bt proteins to protect sugarcane from sugarcane borer in a commercial setting. We have expressed two Bt proteins with differing modes of action (Cry1Ab and Cry2Ab) in commercial sugarcane varieties, demonstrated efficacy against sugarcane borer in the field and describe a strategy for trait deployment in this tropical crop with complex genetics that limits trait introgression by backcrossing.