Extensive Functional Diversification of the<i>Populus</i>Glutathione<i>S</i>-Transferase Supergene Family

Lan, Ting; Yang, Zhi‐Ling; Yang, Xue; Liu, Yan-Jing; Wang, Xiaoru; Zeng, Qing‐Yin

doi:10.1105/tpc.109.070219

Cited by 195 publications

(194 citation statements)

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“…The tandem duplication ratio of NAC genes in this study is relatively lower compared to some other gene families in Populus , which was represented in a considerable higher proportion [71,72]. Interestingly, a similar low retention rate of tandem duplicates was also observed for Populus ARF gene family [71].…”

Section: Resultssupporting

confidence: 65%

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

et al. 2010

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BackgroundNAC (NAM, ATAF1/2 and CUC2) domain proteins are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. NAC transcription factors comprise of a large gene family represented by more than 100 members in Arabidopsis, rice and soybean etc. Recently, a preliminary phylogenetic analysis was reported for NAC gene family from 11 plant species. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, conserved motifs, and expression profiling analysis has been presented thus far for the model tree species Populus.ResultsIn the present study, a comprehensive analysis of NAC gene family in Populus was performed. A total of 163 full-length NAC genes were identified in Populus, and they were phylogeneticly clustered into 18 distinct subfamilies. The gene structure and motif compositions were considerably conserved among the subfamilies. The distributions of 120 Populus NAC genes were non-random across the 19 linkage groups (LGs), and 87 genes (73%) were preferentially retained duplicates that located in both duplicated regions. The majority of NACs showed specific temporal and spatial expression patterns based on EST frequency and microarray data analyses. However, the expression patterns of a majority of duplicate genes were partially redundant, suggesting the occurrence of subfunctionalization during subsequent evolutionary process. Furthermore, quantitative real-time RT-PCR (RT-qPCR) was performed to confirm the tissue-specific expression patterns of 25 NAC genes.ConclusionBased on the genomic organizations, we can conclude that segmental duplications contribute significantly to the expansion of Populus NAC gene family. The comprehensive expression profiles analysis provides first insights into the functional divergence among members in NAC gene family. In addition, the high divergence rate of expression patterns after segmental duplications indicates that NAC genes in Populus are likewise to have been retained by substantial subfunctionalization. Taken together, our results presented here would be helpful in laying the foundation for functional characterization of NAC gene family and further gaining an understanding of the structure-function relationship between these family members.

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Section: Resultssupporting

confidence: 65%

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

et al. 2010

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“…a universal assay to assess whether or not a given enzyme is catalytically active. This observation is clearly reinforced by the range of activities observed in recent surveys of the GST family in Arabidopsis ) and poplar (Lan et al, 2009). Other GST-associated activities have been postulated (Dixon et al, 2010), including intracellular transport of small molecules such as fl avonoids, transient glutathione conjugation to protect reactive metabolites such as porphyrinogens and oxylipins, introduction of sulfur into secondary metabolites such as gluco- Figure 1.…”

Section: Known Catalytic Roles Xenobiotic Detoxificationmentioning

confidence: 52%

Glutathione Transferases

Dixon

Edwards

2010

The Arabidopsis Book

199

222

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The 55 Arabidopsis glutathione transferases (GSTs) are, with one microsomal exception, a monophyletic group of soluble enzymes that can be divided into phi, tau, theta, zeta, lambda, dehydroascorbate reductase (DHAR) and TCHQD classes. The populous phi and tau classes are often highly stress inducible and regularly crop up in proteomic and transcriptomic studies. Despite much study on their xenobiotic-detoxifying activities their natural roles are unclear, although roles in defence-related secondary metabolism are likely. The smaller DHAR and lambda classes are likely glutathione-dependent reductases, the zeta class functions in tyrosine catabolism and the theta class has a putative role in detoxifying oxidised lipids. This review describes the evidence for the functional roles of GSTs and the potential for these enzymes to perform diverse functions that in many cases are not "glutathione transferase" activities. As well as biochemical data, expression data from proteomic and transcriptomic studies are included, along with subcellular localisation experiments and the results of functional genomic studies.

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“…There are a large number of glutathione-S-transferases (GST) genes in photosynthetic organisms and especially in poplar (Lan et al 2009;Lallement et al 2014a). These proteins are involved mainly in cellular detoxification.…”

Section: Biochemical and Structural Studies Of Redox Enzymes In Progressmentioning

confidence: 99%

Structural and functional characterization of tree proteins involved in redox regulation: a new frontier in forest science

Jacquot

Couturier

Didierjean

et al. 2016

Annals of Forest Science

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& Key message This paper describes how the combination of genomics, genetic engineering, and 3D structural characterization has helped clarify the redox regulatory networks in poplar with consequences not only in system biology in plants but also in bacteria and mammalian systems. & Context Tree genomes are increasingly available with a large number of orphan genes coding for proteins, the function of which is still unknown.& Aims and methods Modern techniques of genome analysis coupled with recombinant protein technology and massive 3D structural determination of tree proteins should help elucidate the function of many of the proteins encoded by orphan genes. X-ray crystallography and NMR will be the methods of choice for protein structure determination. & Results In this review, we provide examples illustrating how the above-mentioned techniques improved our understanding of redox regulatory circuits in poplar, the first forest tree species sequenced. We showed that poplar peroxiredoxins use either thioredoxin or glutaredoxin as electron donors toHandling Editor: Jean-Michel Leban Executive summary This review describes the successful use of technologies to overproduce and purify recombinant enzymes from trees with the aim of solving their 3D structures and identifying their molecular interactions either with other proteins or with potential substrates. Currently only ca a dozen of tree genomes have been annotated and released including six forest species, but this will change rapidly with the oncoming release of the chestnut and oak genomes notably. The availability of additional genomes will open the way to identifying the function of a large number of orphan gene products, one of the ways to characterize these functions being to produce and analyze the corresponding protein products. reduce hydrogen peroxide. That glutaredoxin could be a reductant was unknown at the time of this discovery even in other biological organisms and was later confirmed notably by the observation that the two genes are fused in some bacteria and by the resolution of the structure of the bacterial hybrid protein. Similarly, genome analysis coupled to in vitro analysis of enzymatic properties led to the discovery that some plant methionine sulfoxide reductases can also use both thioredoxins and glutaredoxins as electron donors. Besides their disulfide reductase activity, it has been demonstrated that some poplar glutaredoxins are also involved in iron-sulfur center biogenesis and assembly. The original 3D structure determination has been made with poplar glutaredoxin C1 and then confirmed in a variety of other biological organisms including human. Our work also showed that in plants, socalled glutathione peroxidases use thioredoxins and not glutathione as electron donors. This is true for all nonselenocysteine-containing glutathione peroxidases. Finally, connections between the thioredoxin and glutaredoxin systems have been elucidated through the study of atypical poplar thioredoxins. & Conclusion Altogether, these data il...

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Extensive Functional Diversification of thePopulusGlutathioneS-Transferase Supergene Family

Cited by 195 publications

References 58 publications

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

Glutathione Transferases

Structural and functional characterization of tree proteins involved in redox regulation: a new frontier in forest science

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