November 25, 2014

Seminar: Conifer terpenes: Engineering an Ancient Plant Defense Pathway for Renewable Chemicals and Biofuels

This week we were paid a visit by Prof. Gary F. Peter from the University of Florida. Despite a bizarre series of technical hangups, fire alarms, and presentation snafus, Prof. Peter demonstrated great composure and provided us with an excellent summary on the current state of knowledge regarding the metabolic engineering of Loblolly and Slash pine to increase the terpenoid content of trees as a source of biofuels. Unlike cellulosic based biofuels, the largely reduced nature of olefinic terpene hydrocarbons make them a superior source of fuel that does not have the same fermentation requirements of cellulosic starting material. Terpene resins, as Prof. Peter described them, are "cheap enough to burn". In this presentation, he describes a statistical approach to identifying traits linked to higher accumulations of terpene resins in pine using association genetics, functional genomics, and metabolic engineering.

I admit a personal bias on this research topic since I wrote my dissertation on terpene synthases of Loblolly pine. Nonetheless, Prof. Peter did an excellent job of illustrating the need to de-regulate outplanting of transgenic trees for biofuel production, a sustainable solution to providing reliable, carbon neutral energy sources from renewable materials. Interestingly, his research group has made excellent progress on engineering the "motor" of plastidial isoprenoid biosynthesis, the 2C-methylerythritol 4-phosphate (or MEP) pathway. In particular, in collaboration with Jay Keasling and Jack Kirby from the Joint Bioenergy Institute in Berkeley, California, his group has found that upregulation of rate controlling enzymes of the MEP pathway, such as 1-deoxyxylulose 5-phosphate synthase (DXS), is just as effective at increasing terpene accumulation as is the introduction of MEP pathway intermediates through alternative entry point using intermediates common to photosynthesis. One example is a modified form of the E. coli protein RibB, which converts ribulose 5-phosphate into 1-deoxyxylulose 5-phosphate, providing the first committed intermediate of the MEP (at least in plants) from common metabolic intermediates in the plastid without the loss of carbon associated with the DXS reaction, which is partially powered through the elimination of the stable leaving group CO2. This alternative entry point into the MEP pathway represents an improvement on the efficiency of this step and paves the way for future improvements of terpene production in pine. When combined with the considerable genetic resources and traditional breeding programs available in this species, pine is becoming a more and more attractive platform for sustainable, carbon neutral energy production. Everyone at our institute was happy to meet Gary and ask him questions following his presentation. Let's hope the public resistance to using genetically modified organisms to meet our environmental challenges can be overcome by better education so that we can take advantage of these exciting new technologies to make the world a better and cleaner place to live in. Thanks for an excellent presentation, Gary.

October 10, 2014

Seminar: Genes, jeans and genomes: exploring the mysteries of polyploidy in cotton

Today we had the pleasure of hosting Prof. Jonathan Wendel from Iowa State University. Prof. Wendel explains the recent history of cotton domestication and the role that allopolyploidy (genome merging between related species) has played in this process. Cotton is an agronomically important plant that is intimately linked to many aspects of recent human history. Here we learn how diverse the Gossypium genus is in natural populations and how modern comparative genomics tools help us understand not only the history of genome duplication events but also the unexpected effects that allopolyploidy has on transcriptional programs in the hybrid offspring.

September 29, 2014

Tutorial: Mass spectrometry in plant science, part 1 – how a quadrupole produces a mass spectrum

            Mass spectrometry (MS) is one of the most widely used analytical techniques in chemistry, and it has wide applications in plant science. A mass spectrum can be used to identify an analyte (an object of analysis, such as a metabolite) by matching its pattern of mass fragments to the entries in a library of reference spectra. Understanding the fundamental principles behind mass spectrometry enables the proper interpretation of spectra and library search results and may assist in the identification of unknown plant metabolites. What follows is an introduction to the principles behind the experimental acquisition of a mass spectrum using an analyzer commonly found in most plant research institutes.

September 26, 2014

Seminar: Control of recombination and genome engineering in plants

Today, we hosted Prof. Holger Puchta from the Karlsrühe Institute for Technology here at our institute, the Center for Research in Agricultural Genomics. In the video below, he gives us an update on genome engineering in plants.

August 28, 2014

Review: Genomic-scale exchange of mRNA between a parasitic plant and its hosts

ScienceVol. 345 no. 6198 pp. 808-811 

 (click here to access the original article)

 Gunjune Kim1,  Megan L. LeBlanc1,  Eric K. Wafula2, Claude W. dePamphilis2,  James H. Westwood1,*
1Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
2Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA

* Author for correspondence:

We ordinarily think of parasitic organisms living off the nutrients of their host without returning anything of benefit. However, it is another matter to consider that some parasites may not only benefits from host nutrients but acquire their mRNA transcripts as well. Nonetheless, the process of gene acquisition through horizontal gene transfer provides one of several mechanisms by which an organism can acquire a significant amount of DNA from another, so it should come as no surprise to learn that RNA may play a role as an intermediate in some cases. A report last week by groups at Penn State and Virginia Tech, led by James Westwood, describes a parasitic plant, Cuscuta pentagona,  which share significant amounts of mRNA transcripts with two model host organisms, Arabidopsis and tomato.

Kim et al. published the result of extensive RNAseq efforts and host-parasite interactions to characterize the extent of the bidirectional exchange of mRNA molecules through haustoria, specialized organs that facilitate the uptake of nutrients and water by the parasite. Based on their findings, nearly half of the mRNA transcriptome of Arabidopsis could be located in the interface zone between the two species, and many were found in the Cuscuta stem far from their point of origin in the host. While mRNA travel in phloem is well documented, the researchers found not only mRNAs representing species known to travel in phloem but also mRNA species that are typically found only in the cytoplasmic environment.

This indicates that acquisition of novel genes by horizontal gene transfer may in some cases proceed via the intermediacy of RNA, a prospect which so far has been rarely documented. While additional research will provide more insights into how such an exchange of mRNAs may affect the metabolism of the parasite and host, each of which receives a mRNA complement from the other during this exchange, it is tempting to speculate on whether such mRNAs are translated into functional proteins after crossing into the other species. Could a parasite use such mRNAs as metabolic clues to gauge its engagement with its host? Can a parasitic plant send in its own mRNAs to affect the expression of host genes for its benefit? 

Finally, this fascinating reports helps us to redefine what constitutes the boundaries of an organism. It may even have implications for the genetic manipulation of domesticated plants. If the phenomenon described here by Kim et al. is widespread in nature, the concept of different organisms of distinct species exchanging genetic information should not necessarily alarm us if it turns out that mother nature, once again, has done it first, has always done so, and has done so on a scale we can scarcely imagine.

h/t Briardo

August 12, 2014

Review: Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures

The Plant Cell tpc.114.125617  

 (click here to access original article)

Taj Mortona, Jalean Petrickab,c,d, David L. Corcoranb, Song Lib, Cara M. Winterb,c, Alexa Cardab, Philip N. Benfeyb,c, Uwe Ohlerb,e,f,g and Molly Megrawa,b,h,i,*

* Corresponding author:
aDepartment of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon 97331
bInstitute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708
cDepartment of Biology, HHMI and Center for Systems Biology, Duke University, Durham, North Carolina 27708
dDepartment of Biology, Carleton College, Northfield, Minnesota 55057
eDepartment of Computer Science, Duke University, 308 Research Drive, Durham, North Carolina 27708
fDepartment of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, 27710
gBerlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
hDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
iCenter for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331 

The problem of identifying the transcriptional start site (TSS) of a gene is a notoriousluy difficult problem in promoter analysis. In plants, the genetic features which govern where transcriptional initiation will take place have largely been assumed to resemble those identified in more thoroughly studied animal systems. However, a report this week from Molly Megraw's group at Oregon State University (in collaboration with Duke University and Carleton College) describes a large-scale analysis of TSSs using the recently developed technique of paired-end analysis of transcriptional start sites (PEAT). This work alters our view of transcriptional initiation in plants by demonstrating that, in contrast to animal models, most plant promoters are devoid of the TATA box that is typical of TSSs. Instead, transcriptional initiation in plants depends on a large collection of known sequence binding elements.

Previous methods for determining TSSs included a straightforward comparison of ESTs compiled from massive sequence collections. 5'RACE has also typically been employed to determine start sites. However, these techniques are limited by their low throughput nature and reliance on manual production of data on a gene-by-gene basis. 5'RACE is also a finicky technique that lacks reproducibility and so is prone to produce artefacts. A more reliable technique for estimating the true 5' end of transcripts involves the technique of primer extension, one of the more difficult molecular biology techniques to master pertaining to the "old school" skill set.

Morton et al. used paired-ends analysis to generate millions of TSSs from Arabidopsis thaliana root samples. They then analyzed these data using a machine learning model which identified TSS tag clusters with great sensitivity and accuracy. This led then to the analysis of transcription binding sites of promoters showing initiation patterns. Based on these analyses, the authors reached the rather surprising conclusion that TSSs of plants are largely devoid of the canonical TATA box. This work extends our knowledge of transcriptal initiation in plants and provides a tool set for the identification and prediction of TSSs directly from sequence. Having relied personally on 5'RACE and primer extension for years, I extend my gratitude to the authors for making these frustratingly tedious techniques no longer necessary, or at least for providing a reliable alternative.

May 23, 2014

Review: The Origin and Biosynthesis of the Benzenoid Moiety of Ubiquinone (Coenzyme Q) in Arabidopsis

The Plant Cell tpc.114.125807

Anna Blocka, Joshua R. Widhalmb, Abdelhak Fatihia, Rebecca E. Cahoona, Yashitola Wamboldta, Christian Elowskya, Sally A. Mackenziea, Edgar B. Cahoona, Clint Chappleb, Natalia Dudarevab and Gilles J. Basseta,*

* Corresponding author (

aCenter for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
bDepartment of Biochemistry, Purdue University, West Lafayette, Indiana 47907

Ubiquinone belongs to a family of prenylated quinone redox co-factors that are essential electron  and proton carriers in most organisms. While the biosynthesis of the prenyl side chain which anchors it to the mitochondrial membrane is fairly well understood, the biosynthesis of the benzenoid ring has long mystified plant scientists. In bacteria, the benzenoid ring is synthesized from 4-hydroxy benzoate, itself a derivative of chorismate. In fungi, the same moiety is made from para amino benzoic acid (pABA). Work headed by University of Nebraska scientist Gilles J. Basset reports this week a major advance in our understanding of the biosynthesis of the benzenoid ring of ubiquinone in plants. Using Arabidopsis thaliana, they showed that the benzenoid ring can come from either phenylalanine or tyrosine, two fully independent routes, while phenylalaine appears to provide the bulk of substrate leading to the final redox co-factor.