Advances in Enzymology and Related Areas of Molecular Biology, Volume 60

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Additionally, it has been shown that transforming wild-type plants with a truncated ETR lacking the entire histidine kinase domain was sufficient to cause ethylene insensitivity Gamble et al. This hypothesis was further supported by a cleverly designed experiment which used a point-mutated kinase-inactive form of ETR1 to rescue the double LOF etr ; ers mutant Wang et al. The histidine kinase domain of the ethylene receptors has been shown to be important for the association of the receptors with CTR1 or CTR1-like proteins from both Arabidopsis and tomato Clark et al.

Qu and Schaller demonstrated that a truncated ETR1 1— lacking the histidine kinase and receiver domain failed to rescue a triple receptor LOF mutant etr;etr;ein , while the truncated ETR1 1— lacking only the receiver domain was able to restore normal growth of the triple mutant in air, but the plant then became hypersensitive to ethylene Qu and Schaller, In addition, the kinase-inactive form of ETR1, which had been successfully used to rescue the double receptor LOF mutant by Wang et al.

Binder et al. They demonstrated that the LOF mutations in ETR1, ETR2, and EIN4 significantly prolonged the time for recovery of growth rate after ethylene was removed, while the ers;ers double mutant had no effect on recovery rate. Cho and Yoo showed that the histidine kinase activity of the ETR1 ethylene receptor promotes plant growth. Together, these results suggest a very different model for receptor action in which both the histidine kinase and receiver domain are essential.

The solution to this controversy could lie in the structure of the ers allele used to construct the double receptor LOF mutant Wang et al. However, if the histidine kinase activity was essential, how could a truncated ETR lacking both a histidine kinase and receiver domain, referred to as ETR 1— , cause dominant ethylene insensitivity in the wild type?

Xie et al. The result showed that ETR 1— was only functional in etr;ers but not in etr;ers This suggested that the truncated ETR1 without the histidine kinase domain must rely on the remaining ERS1, which has the histidine kinase activity, to repress ethylene signalling. The findings of Xie et al. Moreover, it has previously been shown in both Arabidopsis and tomato that only subfamily I receptors were capable of interacting strongly with the downstream CTR1 and CTR1-like proteins in the yeast two-hybrid assay Clark et al.

So was it possible that the truncated ETR and the subfamily II receptors could tap into the signalling output of the subfamily I receptors through direct protein—protein interaction? Using a mating-based split-ubiquitin system, Grefen et al. Interestingly, the interaction between ETR1 and the tagged ERS2 can be disrupted by SDS, which suggests that the ethylene receptors can exist as a higher order non-covalent complex. It was hypothesized that this interaction could be mediated by the GAF domain, since truncated receptors lacking this domain could not dimerize when expressed in yeast Xie et al.

At present, the exact function of the receptor histidine kinase domains and the role of the receptor heterodimer interaction in ethylene signalling are still open questions. The solubility in lipid and aqueous phases and the diffusible nature of ethylene gas makes it unnecessary for plants to restrict the ethylene receptors to a specific subcellular compartment to perceive the signal molecule.

Chen et al. AtETR1 was also observed subsequently in the Golgi apparatus and co-localized with RTE1 in roots by immunostaining and fluorescence microscopy Dong et al. On the other hand, the tobacco ethylene receptor NTHK1 was found to be in the plasma membrane Xie et al. Care should be taken, however, when interpreting the results of such experiments, which relied on overexpression of the target protein using a strong CaMV 35S promoter.

To rule out the possibility that these observations were mislocalization artefacts caused by saturation of the endogenous secretion pathway, further studies are needed to investigate their localization under native conditions. The N-termini of the ethylene receptors were predicted to be facing the extracytosolic space the ER lumen with the C-termini exposed to the cytosol, based on the topography of the melon CmERS1 ethylene receptor Ma et al.

In the case of the Arabidopsis ctr , this point mutation within the CN-box can cause a constitutive ethylene response in air, a phenotype resembling the ctr1 null mutation. This suggested that the interaction between ethylene receptors and CTR1, and possibly the subsequent recruitment of CTR1 to the ER membrane by this interaction, is essential for CTR1 function in repressing the downstream ethylene response. However, ethylene treatment does not change the association of CTR1 with the receptors, neither does it change its ER localization.

Thus the question as to how ethylene receptors regulate the activity of CTR1 remains unanswered. Knowing the importance of the histidine kinase activity of the ethylene receptors, one emerging hypothesis is that receptors might have multiple functions. Secondly, in the absence of ethylene, the receptors might utilize histidine kinase activity to phosphorylate CTR1, either directly or through a chaperone protein s , which then activates CTR1 and suppresses the downstream ethylene response pathways.

In this case, ethylene binding might induce a conformational change in the receptor, which diminishes its histidine kinase activity thereby relieving the repression of the downstream pathway. It is well known that binding of phosphatidic acid PA to mammalian Raf-1 can lead to its translocation from the cytosol to the plasma membrane and that CTR1 can also bind to PA Testerink et al.

This new finding raised the question as to whether plant CTR proteins are regulated in a similar manner. Testerink et al. However, yeast two-hybrid experiments have previously shown that only the N-terminus of CTR1 can interact with the ethylene receptors Clark et al. Using yeast two-hybrid assays, Zhong et al. It is not yet clear, however, whether LeCTR1, 3 and 4 are functionally redundant or whether they have unique roles.

The transgenic plants also displayed enhanced susceptibility or enhanced hypersensitive response to the fungal pathogen Botrytis cinerea Fig. Although there was no noticeable change in ethylene synthesis, levels of mRNAs from the ethylene-responsive genes E4 and chitinase B were higher than in the wild type, and pathogenesis-related PR gene transcripts also increased in abundance.

Interesting, Liu et al. Overexpression of the LeCTR2 N-terminus in tomato resulted in developmental abnormality and enhanced hypersensitive response to Botrytis cinerea infection. C Increased hypersensitive response to B. A A simplified structure of LeHB-1 protein with amino acids numbered.

HD, homeodomain; Zip, leucine zipper domain. A fold excess of unlabelled competitor was able to compete the binding lanes 4 and 8.

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Lanes 1 and 5: free probe. D Developmental abnormalities caused by ectopic LeHB-1 expression including development of multiple flowers or double carpel-like structures within one sepal whorl panels 1 and 2 , formation of fruits from sepals panels 3 and 4 and petioles panel 5 , compared with the control panel Ctl. These effects were only observed with a full-length LeHBcoding sequence and were not seen using a construct with an engineered premature stop codon Lin et al.

The lack of any major effect on fruit ripening and triple response, however, indicates that the main role of LeCTR2 involves a specific branch of ethylene signalling Lin et al. It is not known whether the Arabidopsis disease resistance protein EDR1 binds ethylene receptors, but it has been suggested to function as a point of cross-talk between ethylene and salicylic acid signalling Tang et al. Constitutive overexpression of the LeCTR2 N-terminus in tomato led to production of adventitious shoots from leaf rachis and rachillae and formation of leafy inflorescences, suggesting reduced auxin and enhanced cytokinin responses, in addition to the ethylene-related pathways.

This may be due to the effects of persistent overexpression of the LeCTR2 N-terminus, and indicates that there is still much to be learned about cross-talk between ethylene and other plant hormone biosynthesis and signalling networks discussed further in the following sections. It is noteworthy that overexpression of a tomato t etratrico p eptide r epeat protein SlTPR1 , which is believed to operate at the receptor level although it has different receptor-binding characteristics compared with LeCTR2, also produces striking but quite different effects Lin et al , c ; Fig.

In the current ethylene signalling model, receptors are negative regulators. Therefore, ethylene sensitivity could be increased if the receptors were eliminated or down-regulated. This was supported by an early observation that transgenic tomato with reduced ethylene receptor levels ripened early, which was caused by increased ethylene sensitivity Tieman et al. Klee and his co-workers demonstrated that tomato plants could use receptor degradation to modulate ethylene responses Kevany et al.

They also showed that receptor degradation requires ethylene binding, since pre-treatment with the competitive inhibitor 1-MCP could stabilize the receptors. Receptor degradation can also be blocked by MG, a peptide aldehyde, which inhibits the chymotrypsin-like activity of the 26S proteasome Kevany et al. Protein ubiquitin—26S proteasome-associated degradation has already been shown to regulate ethylene biosynthesis see previous sections.

Overexpression of this gene in plants causes a variety of phenotypes suggesting altered hormone responses. A related protein has been identified in Arabidopsis, and shown by in vivo co-immunoprecipitation to bind receptor ERS1 dimers in the cell membrane Z Lin et al.

Alternatively, it is also possible that SlTPR1 functions as an adaptor for receptor degradation, leading to enhanced ethylene sensitivity Fig. Ethylene has been reported to be involved in senescence reviewed by Lim et al. The promotion of flowering by ethylene was first observed in pineapples in thes, and it has become an important horticultural practice for production of pineapple and other bromeliads Abeles et al.

In Arabidopsis , mutants that either overproduce ethylene, such as eto1 , 2 , and 3 , or constitutively switch on ethylene responses, such as ctr1 , have reduced fertility Bleecker et al. In addition to being linked to flower senescence and abscission, it has been known for a long time that ethylene is also implicated in pollination and fertilization. In most species, pollination is accompanied by an increase in ethylene evolution in the stigma and style within hours after pollination and well before pollen germination, and also there is a burst of ethylene synthesis shortly after fertilization.

These results are consistent with ethylene having a fundamental role in flower development, and many studies have indicated that ethylene, together with auxin, plays important roles in pollination-regulated developmental responses and participates in the inter-organ coordination of diverse components of pollination-regulated flower development reviewed by O'Neill, It has been proposed that flowering is triggered by a small burst of ethylene production in the meristem in response to environmental cues and, indeed, the pineapple Ananas comosus AcACS2 was shown to be induced in the meristem during induction of flowering Trusov and Botella, In normal growth and development, the expression of ethylene biosynthesis genes appears to be related to development of particular floral organs.

In situ hybridization experiments revealed that ACO mRNAs were specifically localized to the secretory cells of the stigma and the connective tissue of the receptacle, including the nectaries. Treatment of young floral buds with ethylene led to the accumulation of ACO transcripts in cells surrounding the embryo sac of the ovules Tang et al.

Antisense suppression of the ethylene receptor PhETR2 in Petunia led to stomium degeneration and anther dehiscence before anthesis, indicating that PhETR2 regulates synchronization of anther dehiscence with flower opening Wang and Kumar, In tobacco, ACO transcripts were detected particularly in stigma, style, and ovary, but not in pollen and anthers, and during the early developmental stage, ACO expression occurred preferentially in the funiculus, the integument primordia, and the nucellus of the ovules De Martinis and Mariani, The expression of mRNAs for specific ethylene receptors has also been shown to occur in particular cells.

In Arabidopsis , the expression of the ethylene receptor ETR2 gene was higher in the inflorescence, floral meristems, and developing petals and ovules, suggesting a possible tissue-specific role for ETR2 Sakai et al. The precise timing of flowering can be controlled by multiple environmental and endogenous factors, and the formation and development of flowers involves a genetic network in shoot meristems that specifies floral identity. There is now increasing evidence, at least in some species, that ethylene is involved in this genetic network.

Interestingly, ectopic expression of TAG1 in transgenic plants caused sepals to become fruit like Pnueli et al. Ando et al. Thus the genetic network of floral organogenesis seems to involve ethylene Fig. Furthermore, Lin et al. This is presumably because overexpressing LeHB-1 elevated ethylene production through its transcriptional activation of LeACO1 , although it is likely that LeHB-1 also regulates other important genes. Ethylene-generating compounds such as ethrel [ eth ylene rel easer ethrel , also called ethephon] have been used to cause male sterility in wheat Rowell and Miller, ; Hughes et al.

In cucumber Cucumis sativus , exogenous application of ethylene increases femaleness, and gynoecious genotypes those that produce female flowers only were reported to produce more ethylene Iwahori et al. Kamachi et al. In gynoecious plants and under female inductive conditions, CsACS is expressed in pistil primordia, whereas in monoecious plants that have separate male and female flowers on the same plant , the CsACS transcripts are reduced and accumulate below the pistil primordia on the adaxial side of the petals Kamachi et al. Furthermore, the timing of the induction of expression of the CsACS2 gene at the apex corresponded to the timing of the action of ethylene in the induction of the first female flower at the apex of individual gynoecious cucumber plants.

Yamasaki et al. Their expression patterns correlated with the expression of the CsACS2 gene and with ethylene evolution in the shoot apices of the two types of cucumber plants, and accumulation of CsETR2 and CsERS mRNA was significantly elevated by the application of ethrel to the shoot apices of monoecious cucumber plants. Thus, there is a strong possibility that the induction of femaleness by ethylene in cucumber plants is related to regulatory effects of ethylene on expression of specific floral organ identity genes, although this remains to be determined.

In contrast to its feminizing effect in cucumber, in watermelon Citrullus spp , ethylene promotes male flower development. Salman-Minkov et al. No discernible differential floral sex-dependent expression pattern was observed for this gene; in contrast, the CitACS3 gene was expressed in open flowers and in young staminate floral buds male or hermaphrodite , but not in female flowers. CitACS3 was also up-regulated by ACC, and was thus thought likely to be involved in ethylene-regulated anther development.

Andromonoecy is a widespread sexual system characterized by plants carrying both male and bisexual flowers. In melon Cucumis melo , this sexual form is controlled by the identity of the alleles at the andromonoecious a locus. Cloning of the a gene by Boualem et al. Based on these findings it was concluded that CmACS-7 is the andromonoecious gene and that an active CmACS-7 enzyme is required for the development of female flowers in monoecious lines, whereas a reduction of enzymatic activity results in bisexual flowers in andromonoecious lines.

In melon female flowers, stamen arrest occurs at stage 6 just after the elaboration of carpel primordia. Using in situ hybridization, Boualem et al. Because the CmACS-7 expression level and pattern were not different between female and hermaphrodite flowers and because the loss of CmACS-7 activity accounts for the functional variation, they concluded that CmACSmediated ethylene production in the carpel primordia affects the development of the stamens in female flowers but is not required for carpel development. L, leaf; S, stem; Mfl, male flower; Hfl, hermaphrodite flower; Ffl, female flower.

C, carpel; St, stamen; P, petal; S, sepal. Hybridization signals are marked by arrows; note the absence of signals in male flowers from Boualem et al. A potential genetic regulatory network centred on ethylene governing flower development and reproduction in tomato. The transcription factors CNR and NOR are known to regulate ripening, but it is not yet clear whether they are directly involved in modulating development or ethylene production.

Some bacteria and fungi also produce ethylene, although its role in these organisms is less well understood. It was recently reported that ethylene plays an important role in zygote formation in the cellular slime mould Dictyostelium mucoroides Amagai et al. Dictyostelium mucoroides-7 Dm7 and a mutant MF1 derived from it shows developmental dimorphism, depending upon environmental conditions: macrocyst formation occurs during the sexual cycle, and sorocarp formation during the asexual process.

Amagai et al.

Furthermore, AOA aminooxy-acetic acid, an inhibitor of ethylene synthesis , was found to switch development of Dm7 and MF1 cells from macrocyst to sorocarp formation. This raises the intriguing question of whether ethylene has a primitive role in reproduction and sex determination that has been conserved through evolution.

The economic importance of fruit has served as an incentive to study ripening biochemistry, and an understanding of the physiological responses of ripening to ethylene was well established as early as the s Abeles et al. Increased respiration and a burst of ethylene biosynthesis were found in some fruit during ripening, such as tomato, avocado, apple, and banana, which were then classified as climacteric fruit. In contrast, some fruit showed no increase in respiration and ethylene production during ripening, such as strawberry, grape, and citrus, and were classified as non-climacteric fruit.

In general, fruit with the highest respiration rates, such as banana and avocado, tend to ripen most rapidly, and for non-climacteric fruit the general correlation exists between high respiration and short shelf life Tucker and Grierson, ; Tucker, The increase in ethylene production associated with the respiratory increase is autocatalytic and at least in some fruits there is clear evidence that ethylene causes the climacteric.

Central Dogma and Genetic Code

McMurchie et al. System-1 functions during normal vegetative growth, is autoinhibited by ethylene, and is responsible for producing the basal levels of ethylene synthesized by all plant tissues, including non-climacteric fruit. System-2 comes into play during the ripening of climacteric fruit and during petal senescence and, as we now know, this requires the induction of new ACS and ACO isoforms. Members of both gene families show ripening-related expression, and the accumulation of their mRNAs is stimulated by ethylene Barry et al.

The maintenance of system-2 ethylene production is due to the ethylene-dependent induction of LeACS2 Barry et al. This autocatalytic ethylene synthesis initiates enhanced expression of a cascade of ripening genes that affect colour, flavour, texture, aroma, and taste reviewed by Gray et al. Direct evidence for ethylene synthesis being essential for climacteric fruit ripening was established by experiments showing that reduction in the expression of tomato ACS2 and ACO1 in planta by antisense genes inhibited or delayed ripening Oeller et al. Furthermore, it was also shown that the Nr mutant phenotype of tomato was caused by a dominant mutation in the NR ethylene receptor.

This abolishes ethylene binding to the receptor and results in tomato plants that are insensitive to ethylene and produce non-ripening fruit Wilkinson et al. Because the mutant NR receptor cannot bind ethylene, it continues to maintain an active dominant suppression of ethylene responses through its interaction with the tomato CTR proteins. Antisense inhibition of production of the mutant mRNA in the Nr mutant resulted in failure to synthesize the mutant receptor protein, and partially or completely restored ripening Hackett et al.

Thus climacteric fruit ripening is also controlled at the receptor level. Ripening control in non-climacteric fruit was originally thought to be independent of ethylene. Less is known about the mechanisms, but ethylene can affect non-climacteric fruit; for example, ethylene stimulates de-greening of citrus and there is recent evidence for small changes in ethylene biosynthesis genes and the involvement of ethylene in ripening of non-climacteric fruit.

More recently, evidence has been accumulating for a common genetic regulatory mechanism that controls climacteric and non-climacteric ripening. This challenges the concept that non-climacteric fruit ripening is independent of ethylene. Fei et al. It is appropriate to consider ripening as the final phase in the continuous process of flower development and reproduction. Vriezen et al. The results suggested that ethylene, together with other hormones, played an important part in fruit set and ovary development.

Ishida et al. A mutation in this gene caused retardation in tomato fruit ripening similar to that found for the rin mutation. Although NOR has been suggested to function independently of ethylene in the tomato ripening process Adams-Phillips et al. In contrast, the expression of VaHOX1 was not suppressed by 1-MCP, suggesting that it is either upstream of, or independent from, ethylene. It therefore seems that a genetic network involving ethylene and homeotic regulators may control plant reproduction, particularly floral sex determination, fruit development, and ripening Fig.

Ethylene regulates many aspects of plant developmental processes, and it is clear that the diversity of ethylene functions is achieved, at least in part, by its interactions with other hormone signalling pathways. The interactions between ethylene, jasmonic acid, and salicylic acid signalling have been reviewed elsewhere Wang et al.

Early observations showed that ethylene and auxin can each regulate the activities and levels of the other. For example, auxin can reduce the ability of ethylene to accelerate ageing-dependent processes such as ripening and abscission. Auxin [IAA, 2,4-D, and naphthaleneacetic acid NAA ] also increases the rate of ethylene production, for example in etiolated mung-beans Grierson et al. Arteca and Arteca observed that different parts of Arabidopsis plants produced various levels of ethylene in response to IAA treatment, with the highest production by inflorescence stalks. Leaf age also had an effect on IAA-induced ethylene, with the youngest leaves showing the greatest stimulation.

The highest amount of IAA-induced ethylene occurred in the root or inflorescence tip, with regions below this producing less, suggesting that ethylene and auxin synergistically regulate these developmental processes. The apical hook of etiolated dicotyledonous seedlings results from asymmetric growth of its inner and outer sides, and this process is ethylene dependent Raz and Ecker, Etiolated wild-type seedlings grown in ethylene, the ethylene overproduction mutant eto , and the constitutive ethylene response mutant ctr1 all exhibit exaggerated hook curvature Guzman and Ecker, ; Kieber et al.

Auxin has also been shown to regulate seedling apical hook development. Wild-type Arabidopsis seedlings grown in the presence of auxin or the auxin transport inhibitor 1-naphthylphthalamic acid NAP display no hook, and the auxin transport mutant aux1 also disrupts hook formation Roman et al. Lehman et al. Furthermore, the morphology of the hookless hypocotyl was phenocopied by inhibitors of auxin transport and by high levels of endogenous or exogenous auxin.

Ruzicka et al. In tomato, cross-talk between ethylene and auxin was reported to be related to ethylene receptor levels. Whitelaw et al. This is consistent with the observation that enhanced ethylene responses hinder auxin transport. Also, Lin et al. Overexpression of 35S::SlTPR1 in vivo results in a range of developmental abnormalities related to ethylene and auxin, including dwarf plants, epinasty, degenerated flowers and infertility, parthenocarpic fruit, altered leaf and fruit morphology, and altered abscission Lin et al.

Other hormones are known to elevate ethylene biosynthesis, in addition to auxin, such as cytokinins and brassinosteroids Woeste et al. Auxin treatment results in an increase in the level of several ACS transcripts, while cytokinin has been shown to increase ACS5 protein stability Liang et al.

Hansen et al. The induction of ethylene by cytokinin requires the canonical cytokinin two-component response pathway, including histidine kinases, histidine phosphotransfer proteins, and response regulators. With cytokinin, brassinosteroid also acts post-transcriptionally by increasing the stability of ACS5 protein. These data suggest that ACS is regulated by phytohormones through different regulatory inputs that probably act together to adjust ethylene biosynthesis continuously in various tissues and in response to various environmental conditions.

GA is essential for plant growth and development processes. Calvo et al. They observed a drastic increase in FsACO1 expression when seeds were treated with GA 3 or ethephon, but the stimulatory effect of ethephon was reversed by paclobutrazol, a GA biosynthesis inhibitor, suggesting that GA positively regulated the expression of FsACO1. Achard et al. Similarly, it has also been reported Achard et al. Synchronizing flowering time, flower development, and seed dispersal with the environment are of great importance for plant competition and survival.

Regulating appropriate responses to biotic and abiotic environmental stresses are also of critical importance. Ethylene is a key regulatory and signalling molecule in all of these processes and contributes to a plant's fitness for survival. Ethylene mutants, epistasis analysis, and biochemical characterization have provided us with the knowledge to draw linear pictures of the ethylene biosynthesis and signalling pathways, their regulation, and interactions with other hormones.

Arabidopsis has provided the key to unlocking the ethylene black box, but important insights into flower and fruit development and ripening have come from other species. That we are really dealing with a regulatory net, rather than a pathway, has been suspected for a long time, and this is now becoming clear. However, there are still many unresolved aspects of the network. First, at present we know about three transcriptional regulators for ACS and ACO genes LeHB-1, RIN, and LeERF2 but there must surely be many more to discover that control the 15 or more members of these two gene families expressed in different tissues and organs and in response to various environmental and hormonal signals.

Secondly, many details of the precise functions and interactions of the different ethylene receptors, and the multiple CTRs in species such as tomato, remain to be elucidated. Several lines of evidence point to the possible existence of separate ethylene signalling channels, based on the different receptors, multiple CTRs, other receptor-interacting proteins, and the differential expression of some of these components.

The possibility that different protein complexes may regulate separate aspects of the ethylene response requires further investigation. Thirdly, it is clear that ethylene regulates flower organ development, as well as fruit ripening. A potential genetic network involving ethylene and homeotic proteins, including HD-Zip such as LeHB-1 and TM1 and MADS-box proteins such as RIN and TAG1 , may regulate this fundamental developmental process, but the interactions between these parts of the network and other flower organ identity genes require further detailed study. Fourthly, although the regulatory networks are emerging, and we see roles for control of transcription, mRNA and protein degradation, and post-translational modification of proteins, it is not at all clear how the various parts of the network communicate with each other.

Finally, is ethylene a stress hormone, a developmental signal, or both, and is there an evolutionary link to reproduction as suggested by the results with Dictyostelium? Addressing these questions will bring us closer to understanding the function of this simple hormone with such a complex lifestyle.

Work from this laboratory described in this article was funded by the Biotechnology and Biological Sciences Research Council and the University of Nottingham. Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide.

Sign In or Create an Account. Sign In. Advanced Search. Article Navigation. Close mobile search navigation Article Navigation. Volume Article Contents. Ethylene biosynthesis and regulation. Ethylene signalling. Ethylene and development. Ethylene cross-talk with other phytohormones. Concluding remarks. Recent advances in ethylene research Zhefeng Lin. Oxford Academic. Google Scholar. Silin Zhong. Don Grierson. Cite Citation. Permissions Icon Permissions.

Abstract Ethylene regulates many aspects of the plant life cycle, including seed germination, root initiation, flower development, fruit ripening, senescence, and responses to biotic and abiotic stresses. ACC synthase , ACC oxidase , ethylene biosynthesis , ethylene cross-talk , ethylene signalling , flower development , fruit ripening , sex determination , ubiquitin-mediated degradation. Open in new tab Download slide. ACS4, a primary indoleacetic acid-responsive gene encoding 1-aminocyclopropanecarboxylate synthase in Arabidopsis thaliana.

Structural characterization, expression in Escherichia coli, and expression characteristics in response to auxin. Search ADS.

Dr Russell Collighan

Google Preview. The plant stress hormone ethylene controls floral transition via DELLA-dependent regulation of floral meristem-identity genes. Ethylene regulates arabidopsis development via the modulation of DELLA protein growth repressor function. Evidence that CTR1-mediated ethylene signal transduction in tomato is encoded by a multigene family whose members display distinct regulatory features.

Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening. EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis. Ethylene induces zygote formation through an enhanced expression of zyg1 in Dictyostelium mucoroides. Effects of brassinosteroid, auxin, and cytokinin on ethylene production in Arabidopsis thaliana plants.

Differential expression of the 1-aminocyclopropanecarboxylate oxidase gene family of tomato. Ripening in the tomato Green-ripe mutant is inhibited by ectopic expression of a protein that disrupts ethylene signaling. The regulation of 1-aminocyclopropanecarboxylic acid synthase gene expression during the transition from system-1 to system-2 ethylene synthesis in tomato. Ethylene-sensitive and insensitive regulation of transcription factor expression during in vitro tomato sepal ripening. Ethylene biosynthesis by 1-aminocyclopropanecarboxylic acid oxidase: a DFT study.

Expression and characterization of three tomato 1-aminocyclopropanecarboxylate oxidase cDNAs in yeast. Arabidopsis seedling growth response and recovery to ethylene. A kinetic analysis. Insensitivity to ethylene conferred by a dominant mutation in Arabidopsis thaliana. Expression of ACC oxidase promoter-GUS fusions in tomato and Nicotiana plumbaginifolia regulated by developmental and environmental stimuli. A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons. Evidence of a cross-talk regulation of a GA oxidase FsGA20ox1 by gibberellins and ethylene during the breaking of dormancy in Fagus sylvatica seeds.

Structure of 1-aminocyclopropanecarboxylate synthase, a key enzyme in the biosynthesis of the plant hormone ethylene. The eto1, eto2, and eto3 mutations and cytokinin treatment increase ethylene biosynthesis in Arabidopsis by increasing the stability of ACS protein. Arabidopsis ethylene-response gene ETR1: similarity of product to two-component regulators. Constitutive expression of EIL-like transcription factor partially restores ripening in the ethylene-insensitive Nr tomato mutant.

Localization of the ethylene receptor ETR1 to the endoplasmic reticulum of Arabidopsis. Ligand-induced degradation of the ethylene receptor ETR2 through a proteasome-dependent pathway in Arabidopsis. Identification of cDNA clones for tomato Lycopersicon esculentum mRNAs that accumulate during fruit ripening and leaf senescence in response to ethylene. De Martinis. Silencing gene expression of the ethylene-forming enzyme results in a reversible inhibition of ovule development in transgenic tobacco plants. Comprehensive EST analysis of tomato and comparative genomics of fruit ripening.

Mutational analysis of the ethylene receptor ETR1. Role of the histidine kinase domain in dominant ethylene insensitivity. Localization of the Raf-like kinase CTR1 to the endoplasmic reticulum of Arabidopsis through participation in ethylene receptor signaling complexes. Heteromeric interactions among ethylene receptors mediate signalling in Arabidopsisi. The use of transgenic and naturally occurring mutants to understand and manipulate tomato ripening.

Split-ubiquitin system for identifying protein—protein interactions in membrane and full-length proteins. Stimulation of in vitro RNA synthesis by pre-treating plants with auxins is due to auxin-induced ethylene production. Exploiting the triple response of Arabidopsis to identify ethylene-related mutants. Antisense inhibition of the Nr gene restores normal ripening to the tomato Never-ripe mutant, consistent with the ethylene receptor-inhibition model. Identification of a tomato gene for the ethylene-forming enzyme by expression in yeast. Antisense gene that inhibits synthesis of the hormone ethylene on transgenic plants.

Ethylene responses are negatively regulated by a receptor gene family in Arabidopsis thaliana. That is, reduction can be about using reductive methodologies to dig down to lower levels because the thought is that this exercise leads to more reductive explanations and more reductive explanations are better than explanations at higher levels.

Rosenberg 4. Hence, the task of this explanatory reduction is to explain all functional biological phenomena via molecular biology. This particular debate can be understood as an instance of a more general debate occurring in biology and philosophy of biology about whether investigations of lower-level molecular biology are better than investigations of high-level systems biology Baetu a; Bechtel and Abrahamsen ; De Backer, De Waele, and Van Speybroeck ; Huettemann and Love ; Marco ; Morange ; Pigliucci ; Powell and Dupre ; see also the entries on feminist philosophy of biology , philosophy of systems and synthetic biology , and multiple realizability.

Traditionally, philosophers of science took successful scientific explanations to result from derivation from laws of nature see the entries on laws of nature and scientific explanation. On this deductive-nomological account Hempel and Oppenheim , an explanation of particular observation statements was analyzed as subsumption under universal applying throughout the universe , general exceptionless , necessary not contingent laws of nature plus the initial conditions of the particular case.

Philosophers of biology have criticized this traditional analysis as inapplicable to biology, and especially molecular biology. Since the s, philosophers of biology have questioned the existence of biological laws of nature. Smart emphasized the earth-boundedness of the biological sciences in conflict with the universality of natural laws. Without traditional laws of nature from which to derive explanations, philosophers of biology have been forced to rethink the nature of scientific explanation in biology and, in particular, molecular biology. Two accounts of explanation emerged: the unificationist and the causal-mechanical.

Philip Kitcher , developed a unificationist account of explanation, and he and Sylvia Culp explicitly applied it to molecular biology Culp and Kitcher An explanation of a particular pattern of distribution of progeny phenotypes in a genetic cross resulted from instantiating the appropriate deductive argument schema: the variables were filled with the details from the particular case and the conclusion derived from the premises.

Working in the causal-mechanical tradition pioneered by Wesley Salmon , , other philosophers turned to understanding mechanism elucidation as the avenue to scientific explanation in biology Bechtel and Abrahamsen ; Bechtel and Richardson ; Craver ; Darden a; Glennan ; Machamer, Darden, and Craver ; Sarkar ; Schaffner ; Woodward , There are differences between the various accounts of a mechanism, but they hold in common the basic idea that a scientist provides a successful explanation of a phenomenon by identifying and manipulating variables in the mechanisms thereby determining how those variables are situated in and make a difference in the mechanism; the ultimate explanation amounts to the elucidation of how those mechanism components act and interact to produce the phenomenon under investigation.

As mentioned above see Section 2. There are several virtues of the causal-mechanical approach to understanding scientific explanation in molecular biology. Molecular biologists rarely describe their practice and achievements as the development of new theories; rather, they describe their practice and achievements as the elucidation of molecular mechanisms Baetu ; Craver ; Machamer, Darden, Craver Another virtue of the causal-mechanical approach is that it captures biological explanations of both regularity and variation.

Unlike in physics, where a scientist assumes that an electron is an electron is an electron, a biologist is often interested in precisely what makes one individual different from another, one population different from another, or one species different from another. Philosophers have extended the causal-mechanical account of explanation to cover biological explanations of variation, be it across evolutionary time Calcott or across individuals in a population Tabery , Difference mechanisms are regular casual mechanisms made up of difference-making variables, one or more of which are actual difference makers see Section 2.

There is regularity in difference mechanisms; interventions made on variables in the mechanisms that change the values of the variables lead to different outcomes in the phenomena under investigation. There is also variation in difference mechanisms; interventions need not be taken to find differences in outcomes because, with difference mechanisms, some variables are actual difference makers which already take different values in the natural world, resulting in natural variation in the outcomes.

But philosophers have also raised challenges to the causal-mechanical approach. While some argue that systems biology is best explained using mechanisms cf. Boogerd et al. Braillard ; Kuhlmann ; Silberstein and Chemero Processes are ontologically primary.

Recent literature in molecular biology on molecular pathways cf. Boniolo and Campaner ; Brigandt ; Ioannides and Psillos ; Ross seems to be another instantiation of this shift from mechanistic to processual explanations. As discussed earlier in the historical sections, molecular biologists have relied heavily on model organisms see the entry on models in science.

But making inferences from a single exemplary model to general biological patterns has been cause for worry. What grounds do biologists have for believing that what is true of a mere model is true of many different organisms? One answer, provided by Marcel Weber , is that the generality of biological knowledge obtained from studying exemplary models can be established on evolutionary grounds.

According to Weber, if a mechanism is found in a set of phylogenetically distant organisms, this provides evidence that it is also likely to be found in all organisms that share a common ancestor with the organisms being compared. Unlike the aim of exemplary models, the representative aim of a surrogate model is not necessarily to be broad. For example, biomedical researchers frequently expose surrogate models to harmful chemicals with the aim of modeling human disease.

However, if a chemical proves to be carcinogenic in rats, for example, there is no guarantee that it will also cause cancer in humans. Although this problem is not unique to surrogate models, it often arises when biomedical researchers use them to replicate human disease at the molecular level. Consequently, philosophers who write about the problem of extrapolation in the context of molecular biology often focus on such models see, for example, Ankeny ; Baetu ; Bechtel and Abrahamsen ; Bolker ; Burian b; Darden ; LaFollette and Shanks ; Love ; Piotrowska ; Schaffner ; Steel ; Weber ; Wimsatt Within the context of surrogate models, any successful solution to the problem of extrapolation must explain how inferences can be justified given causally relevant differences between models and their targets Lafollette and Shanks Cook and Campbell This method avoids the circle because it eliminates the need to know if two mechanisms are similar.

All that matters is that two outcomes are produced to a statistically significant degree, given the same intervention. For this reason, statistically significant outcomes in clinical trials are at the top of the evidence hierarchy in biomedical research Sackett et al. One problem with relying merely on statistics to solve the problem of extrapolation, however, is that it cannot show that an observed correlation between model and target is the result of intervention and not a confounder.

This approach avoids the circle because the suitability of a model can be established given only partial information about the target. For example, Steel argues that only the stages downstream from the point where the mechanisms in the model and target are likely to differ need to be compared, since the point where differences are likely will serve as a bottleneck through which the eventual outcome must be produced.

One worry, raised by Jeremy Howick et al. For example, there may be an upstream difference that affects the outcome but does not pass through the downstream stages of the mechanism. This problem is taken up again below in Section 3. The resulting big picture account of the experimental model is an aggregate of findings that do not describe a mechanism that actually exists in any cell or organism. Instead, as a number of authors have also pointed out Huber and Keuck ; Lemoine ; Nelson , the mechanism of interest is often stipulated first and then verified piecemeal in many different experimental organisms.

These genetically engineered rodents are supposed to make extrapolation more reliable by simulating a variety of human diseases, e. As Monika Piotrowska points out, however, this raises a new problem. The question is no longer how an inference from model to target can be justified given existing differences between the two, but rather, in what way should these mice be modified in order to justify extrapolation to humans? Piotrowska has proposed three conditions that should be met in the process of modification to ensure that extrapolation is justified.

The first two requirements demand that we keep track of parts and their boundaries during transfer, which presupposes a mechanistic view of human disease, but the third requirement—that the constraints that might prevent the trait from being expressed be eliminated—highlights the limits of using a mechanistic approach when making inferences from humanized mice to humans. As Piotrowska explains,. As our ability to manipulate biological models advances, philosophers will need to revisit the problem of extrapolation and seek out new solutions. The history of molecular biology is in part the history of experimental techniques designed to probe the macromolecular mechanisms found in living things.

Philosophers in turn have looked to molecular biology as a case study for understanding how experimentation works in science—how it contributes to scientific discovery, distinguishes correlation from causal and constitutive relevance, and decides between competing hypotheses Barwich and Baschir In all three cases, the concept of a mechanism is central to understanding the function of experimentation in molecular biology also see the entry on experimentation in biology.

Take discovery. Darden has countered with a focus on the strategies that scientists employ to construct, evaluate, and revise mechanical explanations of phenomena; on her view, discovery is a piecemeal, incremental, and iterative process of mechanism elucidation. In the s and s, for example, scientists from both molecular biology and biochemistry employed their own experimental strategies to elucidate the mechanisms of protein synthesis that linked DNA to the production of proteins. Molecular biologists moved forward from DNA using experimental techniques such as x-ray crystallography and model building to understand how the structure of DNA dictated what molecules it could interact with; biochemists simultaneously moved backward from the protein products using in vitro experimental systems to understand the chemical reactions and chemical bonding necessary to build a protein.

Tudor Baetu builds on the contemporary philosophy of mechanism literature as well to provide an account of how different experiments in molecular biology move from finding correlations, to establishing causal relevance, to establishing constitutive relevance Baetu b. Much recent philosophical attention has been given to the transition from correlation to causal relevance.

On a manipulationist account of causal relevance, some factor X is determined to be causally relevant to some outcome Y when interventions on X can be shown to produce the change in Y. But these one-variable experiments, Baetu cautions, do not necessarily provide information about the causal mechanism that links X to Y. Is X causally relevant to Y by way of mechanism A , mechanism B , or some other unknown mechanism? In a two-variable experiment, two interventions are simultaneously made on the initial factor and some component postulated in the mechanical link, thereby establishing both causal and constitutive relevance.

An experiment is taken to be a crucial experiment if it is devised so as to result in the confirmation of one hypothesis by way of refuting other competing hypotheses.

Advances in enzymology and related areas of molecular biology. Preface.

But the very idea of a crucial experiment, Pierre Duhem pointed out, assumes that the set of known competing hypotheses contains all possible explanations of a given phenomenon such that the refutation of all but one of the hypotheses deductively ensures the confirmation of the hypothesis left standing.

Duhem actually raised two problems for crucial experiments—the problem mentioned above, as well as the problem of auxiliary assumptions, which any hypothesis brings with it; for reasons of space, we will only discuss the former here. Marcel Weber has utilized a famous experiment from molecular biology to offer a different vision of how crucial experiments work. After Watson and Crick discovered the double helical structure of DNA, molecular biologists turned their attention to how that macromolecule could be replicated see Section 1.

The focus was in part on the fact that the DNA was twisted together in a helix, and so the challenge was figuring out what process could unwind and replicate that complexly wound molecule. Three competing hypotheses emerged, each with their own prediction about the extent to which newly replicated DNA double helices contained old DNA strands versus newly synthesized material: semi-conservative replication, conservative replication, and dispersive replication.

They grew E. By then taking regular samples of the replicating E. Moreover, any hypothesis of DNA replication had to satisfy mechanistic constraints imposed by what was already known about the physiological mechanism—that DNA was a double helix, and that the sequence of nucleotides in the DNA needed to be preserved in subsequent generations. For a critique, see Baetu An overview of the history of molecular biology revealed the original convergence of geneticists, physicists, and structural chemists on a common problem: the nature of inheritance.

Conceptual and methodological frameworks from each of these disciplinary strands united in the ultimate determination of the double helical structure of DNA conceived of as an informational molecule along with the mechanisms of gene replication, mutation, and expression. With this recent history in mind, philosophers of molecular biology have examined the key concepts of the field: mechanism, information, and gene. Moreover, molecular biology has provided cases for addressing more general issues in the philosophy of science, such as reduction, explanation, extrapolation, and experimentation.

History of Molecular Biology 1. Concepts in Molecular Biology 2. Molecular Biology and General Philosophy of Science 3. History of Molecular Biology Despite its prominence in the contemporary life sciences, molecular biology is a relatively young discipline, originating in the s and s, and becoming institutionalized in the s and s. He concluded a essay: The geneticist himself is helpless to analyse these properties further.

Weaver wrote, And gradually there is coming into being a new branch of science—molecular biology—which is beginning to uncover many secrets concerning the ultimate units of the living cell…. According to Lily Kay, Up until around molecular biologists…described genetic mechanisms without ever using the term information. Crick —, emphasis in original It is important not to confuse the genetic code and genetic information.

Brenner, letter to Perutz, Along with Brenner, in the late s and early s, many of the leading molecular biologists from the classical period redirected their research agendas, utilizing the newly developed molecular techniques to investigate unsolved problems in other fields. Concepts in Molecular Biology The concepts of mechanism , information , and gene all figured quite prominently in the history of molecular biology.

Phyllis McKay Illari and Jon Williamson have more recently offered a characterization that draws on the essential features of all the earlier contributions: A mechanism for a phenomenon consists of entities and activities organized in such a way that they are responsible for the phenomenon. Stephen Downes helpfully distinguishes three positions on the relation between information and the natural world: Information is present in DNA and other nucleotide sequences.

Other cellular mechanisms contain no information. DNA and other nucleotide sequences do not contain information, nor do any other cellular mechanisms. Molecular Biology and General Philosophy of Science In addition to analyzing key concepts in the field, philosophers have employed case studies from molecular biology to address more general issues in the philosophy of science, such as reduction, explanation, extrapolation, and experimentation.

Rosenberg 4 Hence, the task of this explanatory reduction is to explain all functional biological phenomena via molecular biology. As Piotrowska explains, without the right context, even the complete lack of differences between two mechanisms cannot justify the inference that what is true of one mechanism will be true of another Piotrowska Conclusion An overview of the history of molecular biology revealed the original convergence of geneticists, physicists, and structural chemists on a common problem: the nature of inheritance.

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Advances in Enzymology and Related Areas of Molecular Biology, Volume 60 Advances in Enzymology and Related Areas of Molecular Biology, Volume 60
Advances in Enzymology and Related Areas of Molecular Biology, Volume 60 Advances in Enzymology and Related Areas of Molecular Biology, Volume 60
Advances in Enzymology and Related Areas of Molecular Biology, Volume 60 Advances in Enzymology and Related Areas of Molecular Biology, Volume 60
Advances in Enzymology and Related Areas of Molecular Biology, Volume 60 Advances in Enzymology and Related Areas of Molecular Biology, Volume 60
Advances in Enzymology and Related Areas of Molecular Biology, Volume 60 Advances in Enzymology and Related Areas of Molecular Biology, Volume 60
Advances in Enzymology and Related Areas of Molecular Biology, Volume 60 Advances in Enzymology and Related Areas of Molecular Biology, Volume 60

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