February 17, 2015

New edition of Taiz and Zeiger's classic text now available "Plant Physiology and Development" (Sinauer Assoc. Publishing)

When I took Plant Physiology as an undergraduate twenty years ago, we used Taiz and Zeiger's 1991 first edition text of the same name. The chapter on terpenoids was written by Jonathan Gershenzon, who at the time was a lab director for Prof. Rodney Croteau at the Institute for Biological Chemistry at Washington State University. Reading that chapter changed my life, as I became interested in this family of natural products as a result and later completed my PhD in Rod's lab. Later as  apost-doc I went to work for Jonathan, who by then had become a Director at the Max Planck Institute for Chemical Ecology in Jena, Germany. It was a profoundly rewarding experience. In fact, I am still studying plant terpenoid biosynthesis as a struggling independent researcher in the harsh landscape of Spain in the age of austerity. It is a profoundly difficult experience. All of those experiences, both good and challenging, are indirectly the result of reading that influential chapter as an undergraduate and feeling a fascination for a subject that no other really compared to at that time.

February 13, 2015

Keith Kloor: "Agricultural researchers rattled by demands for documents"

Until now I have resisted any temptation to address political issues in the modest endeavor that is this blog. Instead, I have focused exclusively on recent reports in the plant literature that might have importance to plant science professionals or students of plant biology. I also include research seminars from eminent scientists that visit our institute. In addition, I have a number of educational posts either up or in the works, which I hope to complete between awaiting manuscripts that want finishing. Today, however, I would like to mention a political issue with some relevance to plant science since it impacts the way we conduct research and reveals an important chasm between the public understanding of what we do and what we do. I refer to a recent news item by journalist Keith Kloor published this week in Science.

Zhou et al. "Arabidopsis OR proteins are the major posttranscriptional regulators of phytoene synthase in controlling carotenoid biosynthesis "

Xiangjun Zhou, Ralf Welsch, Yong Yang, Daniel Álvarez, Matthias Riediger, Hui Yuan, Tara Fish, Jiping Liu, Theodore W. Thannhauser, and Li Li

Phytoene synthase (PSY) has long been considered the rate limiting step in the formation of carotenoids, C40 isoprenoid compounds which act as auxiliary pigments in photosynthesis, quenching highly excited chlorophyll and preventing photooxidative damage to chloroplasts. In the human diet, carotenoids are considered both essential nutrients (beta-carotene serves as provitamin A) as well as generally beneficial antioxidant neutraceuticals due to their electron donating (and free radical scavenging) properties. Increasing the accumulation of carotenoids in crops has been a biotechnological goal for some time, and it is clear that PSY modulation will be an important part of this process. But the control of flux though the long and fairly complex carotenoid biosynthetic pathways is tightly regulated, resisting obvious attempts at increasing carotenoid accumulation through simple overexpression. Here Zhou et al. provide an important advance in understanding the posttranscriptional regulation of PSY in plants, which is mediated by the OR (Orange) protein and a small group of partially redundant, related proteins (OR-like) that regulate PSY activity through protein-protein interactions using a combination of yeast 2-hybrid assays, bimolecular fluorescence complementation, and mutant analysis.

Early Edition: Xiangjun Zhou, doi: 10.1073/pnas.1420831112
The original article can be found here

From the article:

February 11, 2015

Boutanaev et al. "Investigation of terpene diversification across multiple sequenced plant genomes"

Alexander M. Boutanaev, Tessa Moses, Jiachen Zi, David R. Nelson, Sam T. Mugford, Reuben J. Peters, and Anne Osbourn

This actually came out the end of last year, but since terpene synthases have been a theme lately, this one is well worth including. Boutanaev et al. used comparative genomics to identify associations between two groups of enzymes that are important for making terpenes: terpene synthases (TS), which generate olefinic hydrocarbons or alcohols from prenylated diphosphate precursors of varying chain lengths, and cytochrome P450s (CYPs), which introduce various oxygen functionalities into the carbon skeleton through regiospecific oxidation reactions once the diphosphate has been removed.  By comparing TS/CYP gene pairs from many sequenced plant genomes, they determined that the evolution of terpenoid biosynthetic pathways, which requires TS and CYP activities among others, has occurred differently in monocot and dicot lineages. In monocots, individual TY and CYP genes were recombined in dynamic genome rearrangements whereas new terpenoid diversity was acquired in dicots by gene duplication and subfunctionalization of TS/CYP pairs. Their approach also facilitated the identification of functional pairing of TS and CYP genes in previously unknown gene clusters.

vol. 112 no. 1 Alexander M. Boutanaev,  E81–E88, doi: 10.1073/pnas.1419547112
The original paper can be seen here 

From the article


Plants produce an array of specialized metabolites, including chemicals that are important as medicines, flavors, fragrances, pigments and insecticides. The vast majority of this metabolic diversity is untapped. Here we take a systematic approach toward dissecting genetic components of plant specialized metabolism. Focusing on the terpenes, the largest class of plant natural products, we investigate the basis of terpene diversity through analysis of multiple sequenced plant genomes. The primary drivers of terpene diversification are terpenoid synthase (TS) “signature” enzymes (which generate scaffold diversity), and cytochromes P450 (CYPs), which modify and further diversify these scaffolds, so paving the way for further downstream modifications. Our systematic search of sequenced plant genomes for all TS and CYP genes reveals that distinct TS/CYP gene pairs are found together far more commonly than would be expected by chance, and that certain TS/CYP pairings predominate, providing signals for key events that are likely to have shaped terpene diversity. We recover TS/CYP gene pairs for previously characterized terpene metabolic gene clusters and demonstrate new functional pairing of TSs and CYPs within previously uncharacterized clusters. Unexpectedly, we find evidence for different mechanisms of pathway assembly in eudicots and monocots; in the former, microsyntenic blocks of TS/CYP gene pairs duplicate and provide templates for the evolution of new pathways, whereas in the latter, new pathways arise by mixing and matching of individual TS and CYP genes through dynamic genome rearrangements. This is, to our knowledge, the first documented observation of the unique pattern of TS and CYP assembly in eudicots and monocots. 

February 10, 2015

Concetta et al. "Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development"

Maria Concetta Palumbo, Sara Zenoni, Marianna Fasoli, Mélanie Massonnet, Lorenzo Farina, Filippo Castiglione, Mario Pezzotti, and Paola Paci


Plant Cell 2015 26: 4617-4635. First Published on December 9, 2014; doi:10.1105/tpc.114.133710


We developed an approach that integrates different network-based methods to analyze the correlation network arising from large-scale gene expression data. By studying grapevine (Vitis vinifera) and tomato (Solanum lycopersicum) gene expression atlases and a grapevine berry transcriptomic data set during the transition from immature to mature growth, we identified a category named “fight-club hubs” characterized by a marked negative correlation with the expression profiles of neighboring genes in the network. A special subset named “switch genes” was identified, with the additional property of many significant negative correlations outside their own group in the network. Switch genes are involved in multiple processes and include transcription factors that may be considered master regulators of the previously reported transcriptome remodeling that marks the developmental shift from immature to mature growth. All switch genes, expressed at low levels in vegetative/green tissues, showed a significant increase in mature/woody organs, suggesting a potential regulatory role during the developmental transition. Finally, our analysis of tomato gene expression data sets showed that wild-type switch genes are downregulated in ripening-deficient mutants. The identification of known master regulators of tomato fruit maturation suggests our method is suitable for the detection of key regulators of organ development in different fleshy fruit crops.

February 9, 2015

Niewenhuizen et al. "Natural variation in monoterpene synthesis in kiwifruit: transcriptional regulation of terpene synthases by NAC and EIN3-like transcription factors"

Niels J. Nieuwenhuizen, Xiuyin Chen, Mindy Y. Wang, Adam J. Matich, Ramon Lopez Perez, Andrew C. Allan, Sol A. Green, and Ross G. Atkinson

Plant Physiol. pp.114.254367; First Published on February 3, 2015; doi:10.1104/pp.114.254367

From the article:
Two kiwifruit (Actinidia) species with contrasting terpene profiles were compared to understand the regulation of fruit monoterpene production. High rates of terpinolene production in ripe A. arguta fruit were correlated with increasing gene and protein expression of a terpene synthase AaTPS1 and correlated with an increase in transcript levels of the MEP pathway enzyme 1-deoxy-D-xylulose-5-phosphate synthase (DXS). In A. chinensis, AcTPS1 was identified as part of an array of eight tandemly duplicated genes and AcTPS1 expression and terpene production was observed only at low levels in developing fruit. Transient over-expression of DXS in tobacco leaves elevated monoterpene synthesis by AaTPS1 >100-fold, indicating that DXS is likely to be the key step in regulating MEP substrate flux in kiwifruit. Comparative promoter analysis identified potential NAC and EIN3-like transcription factor (TF) binding sites in the AaTPS1 promoter, and cloned members of both TF classes were able to activate the AaTPS1 promoter in transient assays. Electrophoretic mobility shift assays showed that AaNAC2, 3 and 4 bind a 28 bp fragment of the proximal NAC binding site in the AaTPS1 promoter but not the AcTPS1 promoter, where the NAC binding site was mutated. Activation could be restored by re-introducing multiple repeats of the 12 bp NAC core-binding motif. The absence of NAC transcriptional activation in ripe A. chinensis fruit can account for the low accumulation of AcTPS1 transcript, protein and monoterpene volatiles in this species. These results indicate the importance of NAC transcription factors in controlling monoterpene production and other traits in ripening fruits.