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  2. Background
  3. Epigenetic and developmental regulation in plant polyploids.
  4. Regulation of gene expression

Whether these effects, observable under controlled conditions in the laboratory, have any influence in the field is yet to be tested. Because the function of these proteins in RNA processing is highly general, however, it is not always clear whether these effects are mediated by the influence of the autonomous pathway genes on FLC gene expression levels. Nonetheless, the fact that variation at these genes affects so many traits, some of which are associated with seasonally variable stressors such as drought, cold, and pathogen load, raises the possibility of the correlated regulation of seasonal phenology and tolerance to seasonal environmental factors.

The seasonal timing of developmental transitions such as flowering, germination, or budbreak can have strong fitness consequences, because different life stages have different environmental tolerances or optima. For this reason, it is beneficial for plants to time the transition from one life stage to another so that each life stage is matched to the environment that it can tolerate. To maintain coordination with external environmental cues, plant developmental transitions are regulated by internal and external environmental signals, and the signaling pathways involved have pleiotropic effects on developmental transitions across multiple life stages.

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The seasonal regulation of flowering time requires halting of development until some stimulus alleviates that repression. Winter bud dormancy also mediates iteroparity in perennial species, and homologs of A. Unlike the irreversible suppression of weak FLC haplotypes in A. As such, PEP1 is essential for the expression of a perennial and iteroparous life history. Another critical point of developmental arrest in plants is seed dormancy. Dormancy prevents seeds from germinating at inappropriate times of year even though ambient environmental conditions may be temporarily favorable.

Dormancy is induced at the later stages of seed maturation and it is also maintained in seeds after imbibition under certain conditions.

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Thus, many genes in multiple flowering pathways also have pleiotropic effects on germination and dormancy. Because primary seed dormancy is induced during the late stages of seed maturation, the seasonal conditions at the time of reproduction and seed maturation have strong effects on seed dormancy and germination. Moreover, the seed coat, derived from maternal tissue, strongly mediates germination behavior. Environmental signals transmitted to seeds can alter germination responses not only to maternal environmental conditions but also to conditions experienced by seeds themselves.

Given that DOG1 is strongly expressed in seeds in A. One possibility is that developmental checkpoints after the floral transition, but before bolting, exist, similar to those frequently described in perennial plants in which regulation of floral budbreak is the key determinant of flowering time. These examples show that genes involved in the regulation of the transition to flowering are also frequently involved in other developmental transitions and vice versa.

Some of these genes alter qualities of the maternal tissue that surrounds seeds and thereby influence germination; others are known to be diffusible e. FT and possibly transmitted via provisioning to seeds. This phenomenon is likely to be especially important under natural, seasonally variable conditions. Such environmentally induced pleiotropy is presumably common for genes that regulate environmentally cued developmental transitions, such as flowering, budbreak, shoot emergence and seed germination. Such vertical pleiotropy also contributes to genetic correlations and thereby influences evolutionary outcomes Wright, However, many of those examples also showed that environmental conditions during seed maturation can strongly alter the depth of seed dormancy and thereby germination timing.

Under natural seasonally variable conditions, the timing of flowering can determine the photoperiod, temperature, or canopy coverage that plants experience during seed maturation, and these environmental factors can, in turn, induce different degrees of seed dormancy. Under field conditions, such a dynamic would be manifest as pleiotropy, whereby a gene that alters flowering time would also alter seed germination.

The same dynamic applies to other developmental transitions. Such pleiotropy may also indirectly influence nonphenological traits, and indeed any trait that exhibits plasticity to seasonal environments. Thus, one mechanism whereby genes that regulate developmental timing can also influence leaf traits is by determining the seasonal environmental conditions under which leaves develop.

Whereas genetic pleiotropy can be detected under highly controlled laboratory conditions, environmentally induced pleiotropy may be completely invisible unless organisms are permitted to develop under natural seasonally variable conditions. Consequently, pleiotropy is probably much more commonly expressed in the wild than would be predicted from controlled genetic analyses in the laboratory. Inferences on the functional significance of genes studied under controlled laboratory conditions should be made with that in mind.

Likewise, because dormancy determines the season of seed germination, which determines the exposure of seedlings to major flowering cues such as photoperiod or vernalization, dormancy genes may be selected through their effects on flowering time as well as germination time. Incorrect inferences on gene function are likely when indirect mechanisms of pleiotropy, operating through environmental pathways, are not considered. For adaptive life cycles to be expressed, the timing of developmental transitions across the life cycle needs to be coordinated with the changes in seasonal environmental conditions.

By providing an integrated mechanism for environmental responses, pleiotropy may contribute to that coordination.


However, to express adaptive life cycles, different life stages may need to respond independently to environmental cues — responding to the same cue in a different manner or responding to different cues entirely. After all, different developmental transitions necessarily need to occur at different times of year and therefore under different seasonal conditions. How do such independent responses occur when the same genes regulate more than one developmental transition?

Evolutionary constraints of pleiotropy can be mitigated and result in more independent regulation of traits, despite sharing components of genetic pathways. Pleiotropy is likely to be most constraining when entire genetic pathways are shared among traits Fig. In this case, an environmental cue affects a gene, which transmits the environmental signal down the shared pathway, thereby regulating two or more different traits with the shared signal.

More independent environmental responses of traits may occur if one gene responds differently to the same cue to regulate different traits Fig. Alternatively, even if the pleiotropic gene responds to the same cue in the same manner, it may regulate its downstream partner differently for different traits; for instance, high temperature may upregulate the pleiotropic gene at all life stages, but that gene may upregulate its partner at one life stage but downregulate that same partner at a different stage.

The ability of a pleiotropic gene to respond differently to the environment, or to interact with its partner differently, when regulating different traits would permit distinct responses of different traits to the same environmental cue, despite sharing components of genetic pathways. In this manner, potentially detrimental effects of pleiotropy can be mitigated.

Epigenetic and developmental regulation in plant polyploids.

Finally, pleiotropy could be least constraining when genetic pathways diverge soon after the pleiotropic gene e. The more elements in a pathway that regulate only one trait as opposed to both traits , the more opportunity for the independent regulation of those traits by the environment. To understand how constraining pleiotropy is likely to be for adaptive evolution, we need to know the degree to which pleiotropic genes operate in the same manner and in the same genetic pathways at multiple life stages.

Exploring the degree of concordance of the pathways that sense and transduce environmental cues at different developmental stages may elucidate how pleiotropic genes are able to regulate adaptive life cycles. The autonomous pathway appears to show a high degree of concordance in the pathways whereby it regulates germination and flowering Fig. Furthermore, different combinations of double mutants of the autonomous pathway genes show responses suggesting conservation of genetic interactions among flowering and germination.

However, the molecular mechanisms by which they regulate germination might also differ from that displayed in the regulation of flowering. In contrast to the autonomous pathway, several genes in the vernalization pathway appear to have different functions when regulating flowering time vs germination, even with respect to how they interact with FLC. This effect on dormancy is inconsistent with their role as FLC repressors, as a lower FLC level is expected to increase rather than decrease germination.

Some concordance of function has been demonstrated in how these downstream integrators regulate germination. It is interesting to note that the autonomous pathway is cued by many internal cues age, nutritional status and only partially by external cues, unlike the vernalization pathway; whether this difference contributes to its functional concordance across development is not known. Functional diversity of pleiotropic genes across the life cycle certainly occurs, however.

Such diversity appears to occur through multiple mechanisms, from potentially regulating the same interacting partners differently at different life stages, to acting independently of them. Pleiotropic constraints, therefore, can evolve through the evolution of how genes within a pathway interact. Pleiotropic genes can have different functions in their regulation of different traits, as discussed earlier. Can this functional diversity within a single individual in any way contribute to divergence of gene function among taxa?

Although no examples illustrate this evolutionary scenario, to our knowledge, certain key components of that scenario have been documented. First, pleiotropic genes exhibit functional diversity in their regulation of different traits. Although some genes exhibit concordant function when regulating different traits e.

Others may retain partners but interact with them differently when regulating different traits. For instance, a gene may upregulate a partner at one life stage but downregulate it in another e. We conclude that the effect of mutant P is not only embryo-specific but also stage-specific. Furthermore, such decrease is analogous to what was observed in sunflower embryos for transcriptional activation of the same genes by HaHSFA9 compare Fig.

The transgenic plant system Fig. RNase A protection Fig. In addition to the data presented in Figs.

Regulation of gene expression

We thus explored most vegetative organs and tissues in young and adult plants, in the absence and presence of stress heat or drought. We conclude that, within the detection limits in our experimental conditions, the HaHSFA9 protein is expressed only in embryos, and it disappears shortly after seed germination. The accumulation of the HaHSFA9 protein precedes and appears connected to the embryo desiccation phase, when potential target genes reach maximal expression levels see for example Ref.

How Genes are Regulated: Transcription Factors

The strict embryo specificity of protein accumulation Fig. This would be different from animal systems. In humans, only HSF4 has strict tissue-specific protein expression patterns in the lung and brain. However, the functions proposed for hHSF4 in these organs would not be related with embryogenesis 7. Even in the case of HSF2, for which functions related with embryo development have been proposed 2 , expression is ubiquitous at low levels 5. This suggests additional non-embryonic functions of HSF2 in most cell types.

Specific interactions, with different transcription factors, could confer distinct functional specificity to the ubiquitous expression pattern of animal HSFs. An example of this is the interaction between c-Myb factor and HSF3 3 , Expression analyses for the more numerous plant HSFs are still scarce.

For example, for the 21 HSFs predicted from the genomic sequence of A. Some peculiarities have been noted from the published information recently reviewed in Refs. Thus, the higher number of plant HSFs could potentially increase the complexity of interactions with other transcription factors and provide additional functional diversification by evolving distinct specific expression patterns as demonstrated in this work for HaHSFA9. Previous evidence supporting functional specialization of plant HSFs is scarce and connected only to thermotolerance 24 , 25 or to cell death defense This was deduced from the specific effects observed by gain of function 24 or, more recently, by loss of function of different HSFs 25 , This observation is unprecedented for an HSF.

Moreover, as in transgenic tobacco during late embryogenesis the mutant P gene also showed reduced activity, compared with WT, we infer that endogenous HSFs, with similar transcriptional activation properties as HaHSFA9, are present in this system.

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Furthermore, the seed specificity of the effect of mutant P in tobacco would be consistent with HSF s with functions mostly embryonic, as proposed above for HaHSFA9 based in its peculiar expression pattern. The increased basal expression levels observed for the P mutant gene in sunflower embryos, compared with that of WT and m versions Fig. This is consistent with reports reviewed in Ref. Previous work from our laboratory suggested the critical involvement of atypical HSFs in the seed-specific expression of Hahsp The gapped HSEs in both promoters were necessary for their transcriptional activation during late embryogenesis in transgenic tobacco 11 , In the case of Hahsp On the other hand, the Hahsp These HSFs, when individually tested with the Hahsp Our previous studies 10, 11, 12, 16, and 20 did not anticipate the following two properties of HSFs involved in developmental regulation in plants: 1 the embryo specificity, and 2 the detrimental transcriptional effect of HSE consensus improvement.

These two unique properties, together with the efficient activation through the Hahsp The findings reported here open the possibility of investigating functions that have been proposed for such sHSP genes see for example, Ref. This might be achieved by gain-of-function or loss-of-function approaches in transgenic plants using HaHSFA9. The costs of publication of this article were defrayed in part by the payment of page charges. Section solely to indicate this fact.

Almoguera, A. Rojas, J. Prieto-Dapena, R.