The 55th NIBB Conference
Frontiers of Plant Science in the 21st CenturyConference Review |
Reports |
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Report on the Panel Discussion
2. Overcoming genetic redundancy in plants
Barry Causier (University of Leeds, UK) In the post-genomic era of plant research, assigning functions to the large number of identified genes is a daunting task. To compound matters, this task is complicated by genetic redundancy. Plant genomes are subject to global and/or local gene duplication events, resulting in multiple copies of genes within the genome. Although the function of the duplicates may diverge over time, in some cases, a redundant situation arises in which “two or more genes are performing the same function and that inactivation of one of these genes has little or no effect on the biological phenotype” [Nowak et al. (1997) Nature 388, 167]. In studies of gene function, several approaches can be used to overcome redundancy. Classically, gene function might be investigated using a reverse-genetics approach involving the isolation of loss-of-function mutants. In the case of redundancy, mutants in all redundant genes need to be isolated and crossed together to generate a multiple mutant, which has a phenotype that reveals the function of the redundant genes. While this is straightforward when only a few genes are involved, it becomes difficult and time-consuming if numerous genes need to be silenced. An alternative method is to use RNAi or miRNA to silence gene families. In principle, these are simple approaches, but in practice, many pitfalls are encountered, including nontarget effects, transgene silencing, and variable silencing of the target, which need to be taken into account. At the protein level, gene redundancy can be alleviated by the expression of mutated or truncated versions of one of the duplicate genes. These altered proteins may cause dominant negative effects in the cell as they compete with the native proteins (including redundant proteins) for interactions, resulting in loss-of-function phenotypes. Genetic redundancy is a particularly difficult problem in the study of plant transcription factors, some of which exist as very large gene families (see the Plant Transcription Factor Database, http://plntfdb.bio.uni-potsdam.de/v2.0/). Several approaches, in addition to those mentioned above, have been developed to overcome redundancy within these families. Transcriptional activators can be converted to repressors by adding a protein domain that strongly inhibits transcription [such as the SRDX or the engrailed domains; Hiratsu et al. (2003) Plant J. 34, 733; Markel et al. (2002) NAR 30, 4709]. Similarly, repressors can be converted to activators by adding domains that strongly promote transcription [such as VP16; Silveira et al. (2007) Plant Sci. 172, 1148]. In both cases, dominant negative effects may result in loss-of-function phenotypes.
Following speciation, gene duplication events will occur independently in diverged species. Consequently, while multiple genes in one species may perform a particular function, in another, a single gene might carry out the same function. The study of orthologous genes in a species in which less redundancy exists for a function should prove to be a useful alternative to species in which redundancy hinders functional studies.It is becoming clear that the use of a combinatorial methodology that utilizes the advantages of approaches at the DNA, RNA, protein, and evolutionary levels may be the best approach to overcoming genetic redundancy when characterizing gene function. ≫ Audience comments and questions |
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