Dr. Joachim Messing

Plant Genetics

Dr. Joachim Messing is the fourth Director of the Waksman Institute of Microbiology, a University Professor of Molecular Biology, and the first holder of the Selman A. Waksman Chair in Molecular Genetics.

Bio
Since his arrival at Rutgers in 1985, Dr. Messing has been instrumental in initiating many research programs in the Life Sciences at Rutgers. He founded two new departments at Rutgers and served as their founding chair, the Department of Molecular Biology and Biochemistry and the Department of Genetics. Under his leadership, the institute also provided incubation space for two Advanced Technology Centers, the Centers for Agricultural Biotechnology and Advanced Biotechnology and Medicine. Messing spearheaded the development of technological tools for deciphering and engineering genomes from bacteria to man. He and his colleagues developed the so-called "shotgun DNA sequencing" method in the early eighties using universal synthetic primers first with the M13mp series and then the pUC series in conjunction with the JM series of host strains. Because these tools were used throughout the life sciences, his publications became the most frequently cited ones in all sciences for the entire decade of 1981-1990. In 2007, Dr. Messing was inducted as a member of the German Academy of Sciences Leopoldina, the oldest continuously existing scientific association in the world. Membership in the academy is among the highest honors accorded for scientific accomplishment. In 2009, with the creation of the Selman Waksman Chair by the Rutgers Board of Governors, Messing was appointed to this newly endowed chair in acknowledgement of his contributions both to the university and science.

Research Highlights
Besides his early work in molecular biology Messing has focused on plant genetics. His laboratory has studied in particular genes that are expressed during the development of cereal seeds. He is well known for the genomic studies of grass genomes and his laboratory has contributed to the sequencing of rice, sorghum, maize, and Brachypodium. These genomic sequences have permitted his laboratory to study the organization and evolution of the genes that control the supply of proteins for nutrition. More recently, his laboratory has used RNA interference to sudy the role of these proteins in seed development and molecular breeding. One of the new initiatives of his laboratory investigates the potential of sweet sorghum and duckweed as alternative bio-energy sources. Publications are tagged in categories of Bioenergy, Epigenetics, Genome Evolution, Genome Structure, Protein Quality, RNAi, and Shotgun DNA Sequencing. Out of 200 publications prior to 2008 only representative samples are listed.

Recent Publications

Wu, Y, Messing J. 2012. RNA Interference Can Rebalance the Nitrogen Sink of Maize Seeds without Losing Hard Endosperm. PLoS One. 7:e32850. AbstractWebsite

BACKGROUND: One of the goals of plant breeding is to create crops to provide better nutrition for humans and livestock. Insufficient intake of protein is one of the most severe factors affecting the growth and development of children in developing countries. More than a century ago, in 1896, Hopkins initiated the well-known Illinois long-term selection for maize seed protein concentration, yielding four protein strains. By continuously accumulating QTLs, Illinois High Protein (IHP) reached a protein level 2.5-fold higher than normal maize, with the most increased fraction being the zein protein, which was shown to contain no lysine soon after the long-term selection program initiated. Therefore, IHP is of little value for feeding humans and monogastric animals. Although high-lysine lines of non-vitreous mutants were based on reduced zeins, the kernel soft texture precluded their practical use. Kernel hardness in opaque 2 (o2) could be restored in quality protein maize (QPM) with quantitative trait loci called o2 modifiers (Mo2s), but those did not increase total protein levels. METHODS: The most predominant zeins are the 22- and 19-kDa alpha-zeins. To achieve a combination of desired traits, we used RNA interference (RNAi) against both alpha-zeins in IHP and evaluated the silencing effect by SDS-PAGE. Total protein, amino acid composition and kernel texture were analyzed. CONCLUSIONS: The alpha-zeins were dramatically reduced, but the high total seed protein level remained unchanged by complementary increase of non-zein proteins. Moreover, the residual zein levels still allowed for a vitreous hard seed. Such dramatic rebalancing of the nitrogen sink could have a major impact in world food supply.

Xu, JH, Bennetzen JL, Messing J. 2012. Dynamic gene copy number variation in collinear regions of grass genomes. Mol Biol Evol. 29:861-71. AbstractWebsite

A salient feature of genomes of higher organisms is the birth and death of gene copies. An example is the alpha prolamin genes, which encode seed storage proteins in grasses (Poaceae) and represent a medium-size gene family. To better understand the mechanism, extent, and pace of gene amplification, we compared prolamin gene copies in the genomes of two different tribes in the Panicoideae, the Paniceae and the Andropogoneae. We identified alpha prolamin (setarin) gene copies in the diploid foxtail millet (Paniceae) genome (490 Mb) and compared them with orthologous regions in diploid sorghum (730 Mb) and ancient allotetraploid maize (2,300 Mb) (Andropogoneae). Because sequenced genomes of other subfamilies of Poaceae like rice (389 Mb) (Ehrhartoideae) and Brachypodium (272 Mb) (Pooideae) do not have alpha prolamin genes, their collinear regions can serve as "empty" reference sites. A pattern emerged, where genes were copied and inserted into other chromosomal locations followed by additional tandem duplications (clusters). We observed both recent (species-specific) insertion events and older ones that are shared by these tribes. Many older copies were deleted by unequal crossing over of flanking sequences or damaged by truncations. However, some remain intact with active and inactive alleles. These results indicate that genomes reflect only a snapshot of the gene content of a species and are far less static than conventional genetics has suggested. Nucleotide substitution rates for active alpha prolamins genes were twice as high as for low copy number beta, gamma, and delta prolamin genes, suggesting that gene amplification accelerates the pace of divergence.

Wang, W, Messing J. 2012. Analysis of ADP-glucose pyrophosphorylase expression during turion formation induced by abscisic acid in Spirodela polyrhiza (greater duckweed). BMC Plant Biol. 12:5. AbstractWebsite

BACKGROUND: Aquatic plants differ in their development from terrestrial plants in their morphology and physiology, but little is known about the molecular basis of the major phases of their life cycle. Interestingly, in place of seeds of terrestrial plants their dormant phase is represented by turions, which circumvents sexual reproduction. However, like seeds turions provide energy storage for starting the next growing season. RESULTS: To begin a characterization of the transition from the growth to the dormant phase we used abscisic acid (ABA), a plant hormone, to induce controlled turion formation in Spirodela polyrhiza and investigated their differentiation from fronds, representing their growth phase, into turions with respect to morphological, ultra-structural characteristics, and starch content. Turions were rich in anthocyanin pigmentation and had a density that submerged them to the bottom of liquid medium. Transmission electron microscopy (TEM) of turions showed in comparison to fronds shrunken vacuoles, smaller intercellular space, and abundant starch granules surrounded by thylakoid membranes. Turions accumulated more than 60% starch in dry mass after two weeks of ABA treatment. To further understand the mechanism of the developmental switch from fronds to turions, we cloned and sequenced the genes of three large-subunit ADP-glucose pyrophosphorylases (APLs). All three putative protein and exon sequences were conserved, but the corresponding genomic sequences were extremely variable mainly due to the invasion of miniature inverted-repeat transposable elements (MITEs) into introns. A molecular three-dimensional model of the SpAPLs was consistent with their regulatory mechanism in the interaction with the substrate (ATP) and allosteric activator (3-PGA) to permit conformational changes of its structure. Gene expression analysis revealed that each gene was associated with distinct temporal expression during turion formation. APL2 and APL3 were highly expressed in earlier stages of turion development, while APL1 expression was reduced throughout turion development. CONCLUSIONS: These results suggest that the differential expression of APLs could be used to enhance energy flow from photosynthesis to storage of carbon in aquatic plants, making duckweeds a useful alternative biofuel feedstock.

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