Volume 1 Number 2 2007

CONTENTS AND ABSTRACTS

Mitali Banik, Shuyu Liu, Kangfu Yu, Vaino Poysa, Soon J. Park (Canada) Molecular TILLING and EcoTILLING: Effective Tools for Mutant Gene Detection in Plants (pp 123-132)

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Invited Review: Forward genetics has been responsible for our understanding of many biological processes and is an excellent method for identifying genes that function in a particular process. In reverse genetics, the functional study of a gene starts with the gene sequence rather than a mutant phenotype. Using various techniques, a gene's function is altered and the effect on the development and phenotypic traits of the plant is analysed. Reverse genetics is an important complement to forward genetics. For example, using reverse genetics, one can investigate the function of all genes in a gene family, something not easily done with forward genetics. Further, one can study the function of a gene found to be involved in a process of interest in another species, but for which no forward genetic mutants have yet been identified. Finally, the vast majority of genes have not yet been mutated in most plants and reverse genetics allows their study. The availability of complete genome sequences combined with reverse genetics can allow every gene to be studied. In this chapter we review the recent progress that has been made towards identifying induced point mutations and natural variation in different plants using the high throughput reverse genetics technologies, TILLING and EcoTILLING, and discuss the prospects of using these techniques in ornamentals.

Yves Barrière, Cédric Riboulet, Valérie Méchin, Stéphane Maltese, Magalie Pichon (France), Andrea Cardinal (USA), Catherine Lapierre (France), Thomas Lübberstedt (Denmark), Jean-Pierre Martinant (France) Genetics and Genomics of Lignification in Grass Cell Walls Based on Maize as Model Species (pp 133-156)

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Invited Review: Grass lignins are made of guaiacyl and syringyl units together with minor amounts of p-hydroxyphenyl units. The specific association of p-coumaric (pCA) and ferulic (FA) acids to grass lignins has suspected important consequences on wall properties which are however, poorly understood. Genetic variation for lignin content, lignin structure, and p-coumaric and ferulic acid contents has been shown in normal maize, after an earlier description in brown-midrib (bm) mutants. QTL analyses for lignin-related traits have established that nearly 40 genomic regions are involved in maize variation of lignin content. For most of these locations, no candidate genes have been validated, or have been still defined. Whereas all steps of lignin biosynthesis have been presumably identified, little is known about the number of gene members encoding each enzymatic step and the role of each member in organ, stage and/or tissue specificity. Moreover, even if the lignin pathway has often been displayed as a metabolic grid, available results, especially in maize bm and genetically engineered plants, suggest that the hydroxylation/methylation steps at the aromatic C-3 position have a key role in controlling the flux to lignins. Recent studies of cell wall-related gene expression in young and silking maize plants also illustrated an unexpected diversity of genes with differential expression profiles, especially in bm mutants. Breeding maize and other grasses for phenolic structures more suitable for animal nutrition or energy production could now be considered a realistic goal by integrating new genomic-based knowledge on maize lignification.

Cláudia Regina Batista de Souza (Brazil) Genetic and Genomic Studies of Cassava (pp 157-166)

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Invited Mini-Review: Cassava (Manihot esculenta Crantz) is native from South America and is one of the most important tropical foods crops for more than 600 million people worldwide. Cassava storage roots are an excellent source of starch but deficient in proteins, vitamins and other micronutrients. To improve yields, starch quality and nutritional value of cassava roots, many studies have been developed aiming to identify molecular markers and increase knowledge about plant genome and gene function. At present the number of publicity available cassava ESTs is estimated at 36,120. The identification of genes with traits of biological, nutritional and agronomic importance and tissue-specific promoters is essential for biotechnological approaches for cassava improvement, which is underway. In this review important advances in the genetics and genomics of cassava are described.

Yinghui Dan, Zhangjun Fei (USA) Christophe Rothan (France) MicroTom - A New Model System for Plant Genomics (pp 167-179)

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Invited Review: The application of genetic modifications to economically important plant species primarily includes tolerance to broad-spectrum herbicides such as glufosinate or glyophosate, resistance to pest and diseases, high yield, biofuel production and better quality food products for consumption. Plant model systems have played an important role in understanding plant biology that leads to economic trait development in crops. The most highly developed plant model system is Arabidopsis because of its small size, rapid life cycle, small genome, and transformability. MicroTom is a miniature dwarf determinate tomato cultivar, originally bred for home gardening purposes, which shares the major features with Arabidopsis that make it successful as a model system, including small size (up to 1357 plants/m²), short life cycle (70-90 days from sowing to fruit-ripening), relatively small genome (950 Mb) and transformability. In this article we review the current status of the genetic transformation, genome sequencing, functional genomics, reverse genetic tools and improvement of fruit nutrition and flavor quality in MicroTom/tomato, which provides a vision of a new plant model system for functional genomics and its application to economic trait development for crops.

Souleymane Silué, Jean-Marie Jacquemin, Jean-Pierre Baudoin (Belgium) Genes Involved in Phaseolus Embryogenesis (pp 180-192)

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Invited Review: Within the genus Phaseolus, the common bean, Phaseolus vulgaris L., is the most important species widely distributed in the world and occupies more than 90% of production areas sown to Phaseolus species. Interspecific hybridization in the genus Phaseolus, with the aim to introgress desired traits to the common bean, leads to the abortion of immature embryos usually at the globular or early heart-shaped developmental stages. Plant zygotic embryogenesis is controlled by many genes and malfunction of these genes can disrupt embryo formation. In this paper, we reviewed some of these genes i.e. KNOX, BELL1, LEUCINE ZIPPER, PHD-FINGER, GLABRA2, WUSHEL, HEAT SHOCK PROTEIN, LIPID TRANSFER PROTEIN, PASTICCINO, LEAFY COTYLEDON and TITAN, from model plants such as Arabidopsis thaliana, Zea mays, Oryza sativa, Medicago truncatula, Solanum lycopersicum. This study helps us to identify the genes involved in Phaseolus embryogenesis and to verify their expression in ovules at different steps of embryos development.

Guillaume G. Nicolas (Canada), Marc C. Lavoie (Barbados/Canada), Gisèle LaPointe (Canada) Molecular Genetics, Genomics and Biochemistry of Mutacins (pp 193-208)

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Invited Review: Bacteriocins are proteinaceous antibacterial substances produced by bacteria. Mutacins are bacteriocins produced by Streptococcus mutans. Four groups of mutacins have been described to date: lantibiotic monopeptides (bacteriocin Class Ia, Ib) including mutacins B-Ny266, H-29B, K8 (MukA), I, II, III, and 1140; lantibiotic dipeptides (bacteriocin Class Ic) grouping mutacins GS5 (SmbA, SmbB) and BHT-A (BHT-Aa, BHT-Ab); non-lantibiotic monopeptides (bacteriocin Class IIa, IIb) including mutacins BHT-B, F-59.1, I-T9, N and V; and the non-lantibiotic dipeptide (bacteriocin Class IIc) mutacin IV (NlmA, NlmB). Bioinformatic analyses of the S. mutans UA159 genome have revealed genes potentially coding for bacteriocin-like peptides. Lateral gene transfer and recombination contributed to mutacin gene distribution and divergence among strains. Screening of large numbers of isolates has revealed a high polymorphism in the genes encoding mutacin-like inhibitory substances. This emphasises the diversity of antimicrobial substances produced by S. mutans. A relationship between bacteriocins and competence for transformation is emerging. In the future, more research is required to explore the role of mutacin production in the ecology of the oral ecosystem.

Stefan Winter, Elisabeth Simboeck, Christian Seiser (Austria) Open Chromatin (pp 209-225)

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Invited Review: In eukaryotic cells genomic DNA is packaged into chromatin thereby constraining the size of the molecule and allowing the cell to organise the genetic information within the nucleus. However, due to this enormous compaction, the accessibility of particular genomic regions that are required for several fundamental cellular processes such as transcription, replication, DNA repair and recombination is impaired. The reversion of this “locked” state, preparatory to and in the course of such processes, involves numerous epigenetic adaptations that finally embody an open chromatin conformation. These alterations comprise the post-translational modifications of histones as well as the activity of chromatin remodelling complexes and the incorporation of particular non-canonical histone variants although these mechanisms may work as one entity rather than single separated mechanisms. Rapid and transient alterations in the local chromatin structure are distinct from more stable marks that may comprise an epigenetic memory, as they rapidly respond to cellular demands rather than stipulate a particular function. Nevertheless, evidence for an interdependency of histone post-translational modifications, like acetylation, methylation, phosphorylation, ADP-ribosylation and sumoylation, and a role of such “marks” in regulating the accessibility of chromatin, supports the model of a histone code. This hypothesis extends the genetic information by an epigenetic component and regulates the interaction of chromatin with detector proteins. In this review we discuss how the chromatin status is adapted to environmental cues and which factors are involved in the formation and interpretation of open chromatin.

Tanja Zeller, Gabriele Klug (Germany) Bacterial Thioredoxins - Genes and Regulation (pp 226-232)

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Invited Mini-Review: Thioredoxins are small, ubiquitous proteins with a dithiol/disulfide active site (CGPC) and have been characterized in a wide variety of prokaryotic and eukaryotic cells. In the thioredoxin system, thioredoxin reductase serves to reversibly reduce oxidized thioredoxin using NAD(P)H as electron donor. In 1964, thioredoxin was originally discovered as electron donor for ribonucleotide reductase in Escherichia coli. By now, many thioredoxins are identified to fulfil a number of important cellular functions, e.g. they are the major cellular protein disulfide reductases, controlling the cellular redox potential. The multiple and important functions of thioredoxins necessitate to adjust their cellular levels according to the requirements. Despite the importance of thioredoxin functions, only little is known about the regulation of thioredoxin genes. The present review therefore considers bacterial genes encoding thioredoxins. We give an overview on thioredoxin genes and their regulation in different bacteria. Furthermore, we will review the current knowledge about the participation of thioredoxin proteins in the regulation of gene expression and protein activity.