Tuesday, August 7, 2012

New direction on the function of GRAS proteins in gibberellin signaling

Gibberellin GA-1
Gibberellins (GAs) are key plant hormones that regulate various aspects of growth and development of land plants and have been at the center of the “green revolution”. In angiosperms practically every aspect of plant life including seed germination, elongation growth, and flowering are influenced by the action of GAs. In at least some angiosperms, they have a key role in surviving certain stress conditions such as saline environments and cold. In ferns certain GAs (e.g. GA1) or related compounds (e.g. antheridic acid) induce male gametophyte development, might repress the female gametophytes and also play a role in spore germination. Commercially GAs are used in a wide range of applications such as to promote growth of fruit crops, to increase sugar yield in sugar cane and, stimulate malting of barley during beer production. Did you know that almost all seedless grapes and sweet bing cherries are treated with GA derivatives to increase their size?  GAs are also used in “fruit cosmetics” to prevent the undesirable russeting in apples. The next time you visit a plant nursery, note that GA inhibitors are often used to retard growth of nursery plants. As you can imagine given its remarkable uses, the GA pathway is one of the most intensely studied in plant biology and agriculture. It is in this regard that a new story has emerged from research in our group.

Russeting in apples
Research in the past 20 years or so has shown that some of the key players in the GA response pathway  are members of the GRAS family of proteins, which includes proteins such as GA insensitive (GAI), Repressor of GA1-3 (RGA1/DELLA), Short-root, Scarecrow (SCR), and Nodulation Signal Pathway 1 and 2 (NSP1 and NSP2). For a variety of historical reasons, including incorrect domain prediction, GRAS protein were generally believed to function as conventional transcription factors. The original reports that described them as transcription factors were based on flawed recognition of features such as coiled-coil regions, resulting in comparisons between them and bZIP proteins. This was compounded by another erroneous piece of sequence analysis which led to the idea that they might be plant equivalents of the STAT transcription factors (which have P53/cytochrome f fold DNA-binding domains) known from animal and amoebozoans. Consequently, almost all efforts to understand this family have been spent in testing hypotheses arising from this perspective. However, the evidence that GRAS proteins bind DNA is not very rigorous, with several GRAS proteins failing to display the purported DNA-binding activity despite sharing a conserved structure, raising questions about their mode of action and function.

Our recent studies help clarify the situation. We showed that the GRAS family actually belongs to the Rossmann-fold methyltransferase superfamily. We establish that the GRAS family first emerged in bacteria and plant versions represent a case of lateral gene transfer prior to the radiation of land plants. We further show that all bacterial, and a subset of plant GRAS proteins are likely to function as small molecule methylases, but the remaining plant members have lost one or more AdoMet (SAM)-binding residues while preserving their substrate-binding residues. Thus, based on sequence- structure analysis, combined with functional evidence, we predict that GRAS proteins might either modify or bind small molecules, which might include GAs or their derivatives.

Our results have thus falsified the previously-published relationships that were proposed for the GRAS proteins, and more importantly throw a completely new spin on their mode of action in the context of  GA binding or modification. One delicious possibility is that the active versions function as methylases that might modify certain GAs or their derivatives, whereas inactive versions act as GA binding proteins (Experimentalists  take note). While a GA receptor belonging to the alpha/beta hydrolase superfamily has been described previously, the functional evidence suggests that not all aspects of the GA signaling are channelized via that receptor. Hence, the possibility of direct interaction between a GA or its modified derivative with the GRAS methylase domain remains open and a potentially important avenue for signaling. In addition, very little is known of the fate and prevalence of GA methylation which is a mechanism of GA deactivation in angiosperms. The currently characterized GA methylases (GAMT1 and GAMT2) which are also Rossmann-fold methylases belonging to a radiation of plant methylases of ultimately bacterial origin, includes enzymes that methylate carboxy, hydroxyl and amino groups in synthesis of plant metabolites  like caffeine, theobromine, methyl salicylate, and methyl jasmonate among others. In Arabidopsis, these are primarily expressed in the siliques (fruits) including the seeds and are believed to deactivate GAs via methylation and subsequent degradation during the maturation of seeds. One possibility is that such a methylation dependent control of GAs also occurs in other parts and other developmental processes via the action of GRAS family methylases. The possibility of the inactive versions of the GRAS proteins binding methylated or other modified GAs is also an avenue for possible functional studies.

It should be noted that our phylogenetic analysis (see figure above) suggests that the GRAS superfamily was delivered to plants via a single lateral transfer from bacterial prior to the diversification of land plants --  this ancestral plant GRAS protein underwent a lineage-specific expansion into 13 distinct well-supported clades that contained at least one representative from bryophytes, lycopodiophytes and angiosperms. At face value, assuming a direct GA-related role for the GRAS family, this would suggest that the GA-like molecules were already functional in the early history of land plants. This clearly goes contrary to certain suggestions of plant evolutionists that GA-like molecules were absent in bryophytes like Physcomitrella, but supports recent experimental results suggesting a role for GA-like molecules in caulonema formation, growth direction of protonemata, and spore germination these mosses (Hayashi et al). Our findings suggest that the predicted small-molecule binding/modifying activity would extend to the base of land plants and could have bearing on the enigma of the role of GA-like molecules in basal land plants. For more details, you can read our paper here.