Identification and Classification of Senescencerelated Genes

Recent molecular studies have confirmed that the processes of senescence and ripening are accompanied by changes in gene expression. Utilizing differential screening and subtractive hybridization techniques a number of cDNAs that are up regulated during senescence have been cloned. Genes that exhibit enhanced expression during senescence have been cloned from the leaves of Arabidopsis, asparagus, Brassica napus, barley, maize, radish, and tomato (reviewed in Smart, 1994; Buchanan-Wollaston, 1997; Nam, 1997; Weaver et al., 1997; Quirino et al., 2000). Differential screening of senescing petal cDNA libraries and PCR-based differential display techniques have been utilized to identify genes that are up regulated during senescence of carnation and daylily flowers (Woodson et al., 1993; Woodson, 1994; Valpuesta etal, 1995; Guerrero etal., 1998;Panavas etal., 1999). Many mRNAs accompanying fruit ripening have also been identified (Davies and Grierson, 1989; Gray et al., 1992). Table 4-1 includes a listing of those cDNAs identified as senescence-related whose identity has been determined by sequence homology to previously characterized genes published in DNA and protein databases. It is not the intent to provide an exhaustive review of all relevant genes but to present representative examples from multiple systems that will allow us to examine the genetic regulation of senescence from a wider perspective.

Most of the genes that have been identified as senescence-related are expressed at basal levels in non-senescing tissues (green leaves and fruits and young flowers) and increase in abundance during senescence. A smaller number of SR genes are only detectable in senescing tissues and represent senescence or ripening-specific genes. An even smaller set of genes have been identified that have high levels of expression early in development, decreased expression in young maturing tissue and increased expression at the onset of senescence. Genes that fit within this class have only been identified in vegetative tissues and represent genes that have a similar role in multiple stages of development like germination and senescence (Smart, 1994; Buchanan-Wollaston, 1997; Lohman et al., 1994). More detailed classifications of the patterns of gene expression during leaf senescence can be found in reviews by Smart (1994) and Buchanan-Wollaston (1997). A classification based on patterns of gene expression is not given in Table 4-1 of this review because the patterns of expression are often different in leaves, flowers, and fruit.

Recently, concern has been voiced about the method of normalizing the samples run on RNA gels for northern blot analysis of genes in senescing tissues. This concern is based on the fact that massive degradation of RNA occurs during senescence. Therefore expression of a particular mRNA may appear to be up regulated in a senescing tissue when it is merely being maintained at steady levels or is decreasing in abundance less rapidly than the total RNA levels. In response to this concern it has been suggested that normalizing RNA loading on the basis of fresh weight, which is relatively stable until later stages of senescence, might provide a more representative pattern of gene expression during senescence (Nooden et al., 1997). Incomplete extraction and variability in yield between samples following RNA extraction procedures make normalization by fresh weight difficult and have provided the main impetus for normalizations based on total RNA. In this chapter it should be noted that almost all of the reports of up-regulation of gene expression during senescence are based on northern blots normalized by equal RNA loading. This is an issue that should be kept in mind when reporting expression patterns of SR genes and will undoubtedly need to be revisited.

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