|
|
|
       |
  |
|||||||||||||||||||
 |
||||||||||||||||||||
The Big QuestionPlant Biotechnology, functional genomics and genetics focusing on development of plant organs in both legumes (soybean and Lotus japonicus ) and oil palm The Short-term goals We are researching the function of meristems and their ability to interact, thereby controlling plant organ development and performance. Our focus is on the development of the nitrogen fixing nodule in the legume system. Recent application of functional genomics has allowed the isolation of several genes controlling the reception of the bacterial nodulation factor, and internal autoregulation of nodulation. In all cases the affected genes are receptor kinases suggesting that short and long-distance signaling using putative macromolecules such as peptides and small RNA, is critical for plant development. We are attempting to discover the ligands and substrates for the GmNARK receptor kinase altered in AON deficient mutants exhibiting a supernodulation phenotype (see Searle et al, 2003, Science 299:109-112). In parallel we are attempting to isolate the interacting protein of this receptor. The GmNARK gene was also shown to be critical for mycorrhizal colonization of soybean roots. Ethylene also controls the proliferation of nodules, and ethylene-resistant legumes were produced by transgenic approaches (using the AtETR1-1 resistance gene). It is likely that similar regulatory mechanisms control the initiation and proliferation of lateral root meristems. Thus our research focus is to define the genetic regulatory networks controlling nodule initiation, proliferation and lateral root function. Through the analysis of legume root development, we will contribute to the understanding of plant nutrient uptake and metabolism.
Current
Currently active
In development
Top three areas of knowledge
Top three technical skills
My research expertise lies in plant developmental genetics; I intend to understand the mechanisms by which simple cells whether within an embryo or an apical meristems, differentiate into complex structures with complex biochemical repertoires. To do so I have chosen a genetic approach, as this allows the coupling of function (such as a mutant phenotype) to the structure of the control elements (the gene, the protein, the signal molecule). Over the last decade this approach was expanded into a genomic approach, complete with structural and functional aspects. In the last year my research developed to a further level through the discovery of a critical gene controlling cell proliferation at a long distance during the development of nitrogen fixing nodules in soybean (see Searle et al, Science 2003). This gene controlling autoregulation of nodulation is a receptor kinase that suggests mechanism and function. I have moved forward to analyse the complexities linking to protein function with its biochemical signals in an attempt to expand genomic research to the post-genomic era (see Gresshoff, 2003; Genome Biology ). My major contribution to the field are in two areas, which overlap through the technologies commonly called 'Map-based cloning'. Expertise area 1: Genetic contribution of the legume to the nitrogen fixing nodule symbiosis . Essential advances have been summarized in several key reviews receiving up to 350 citations (c.f., Caetano-Anolles and Gresshoff, 1991; Gresshoff, 1993; Plant Breeding Reviews ) and recent papers (Searle et al, 2003; Science ; Wopereis et al, 2000; Plant Journal ; Men et al, 2002; Genome Letters ). My research in the early 1980s initiated the analysis of the plant's genetic contribution through an induced mutagenesis program then funded by the Agrigenetics Corporation and subsequently by a Section 39 grant from the Australian Federal Government (DITEC). We showed conclusively that the plant has the genetic capability to control in the initiation and proliferation of nitrogen fixing nodules (see Carroll et al, 1985a,b; 1986; PNAS ). We isolated and characterized for the first time plant mutants able to form nodules in the presence of nitrate and demonstrated that such mutants have an absence of autoregulation (AON; Day et al, 1986; Physiol. Plant.). We were the first in the world to demonstrate shoot control of autoregulation (Delves et al, 1986; Plant Physiology ) which led to the refinement of leaf control (Delves et al, 1992; Plant &Cell Physiol.). The paradigm shift of the shoot (leaf) led to the concept of long distance regulation of nodulation and the need for long distance signals (the topic of this application). We were the first to map any symbiotic gene in a legume using molecular marker technology (Landau-Ellis et al, 1991; Mol. Gen. Genet.). This was followed by the first physical mapping in any legume using pulse field gel electrophoresis and Not I generated fragments identified by closely linked molecular markers (RFLPs) to calculate for the first time a conversion factor of genetic to physical distance for the soybean genome (Funke et al, 1993, Plant Mol. Biology ). In parallel we developed arbitrary primed PCR (Caetano-Anolles et al, 1991, Biotechnology ) and associated DNA silver staining (Bassam et al, 1991; Anal. Biochemistry ), techniques which are now patented and widely used for identification and mapping. [Promega Inc has commercialized the silver-staining method as the Silver Sequence kit). We were the first to develop BAC clones needed for positional mapping in both soybean and the model legume Lotus japonicus (Pillai et al, 1995; Symbiosis ; Funke et al, 1993; Plant Mol. Biol.), and developed the first BAC library for the model legume Lotus japonicus . In parallel to the genomic analysis of nodulation we initiated transcriptional profiling of gene expression in soybean. We were the first to publish microarray data and methodology for soybean and became the reference point for future analyses (Maguire et al, 2002; J. Plant Physiology ). The analysis of autoregulation reached a significant point through the discovery of the affected gene. This cloning of GmNARK (Nodule autoregulation receptor kinase) was accomplished by positional or map based cloning (Searle et al, 2003, Science ; Men et al, 2002; Genome Letters ). The positional cloning of the GmNARK gene still remains the only published example of positional cloning of any gene in soybean (known to be difficult because of a larger genome size and extensive chromosomal duplications). Although the gene itself was of interest, its suggested function led to more interest including a feature in Nature News and Views (December 2002). GmNARK , the orthologue of the Lotus japonicus gene LjHAR1 (with which we also worked; see Wopereis et al, 2000; Plant Journal ; Jiang and Gresshoff, 2002, Fun ctional Plant Biology ) is a leucine rich repeat receptor kinase, related to LRR kinases such as Arabidopsis CLAVATA1 and the phytosulphokine receptor. This suggests reception of a macro-molecular signal. This in turn suggests that plants may require novel signal cascades of which the GmNARK system is just one. Expertise area 2: DNA profiling: We invented and patented the novel single arbitrary primer DNA profiling method DAF (Caertano-Anolles et al, 1991; Biotechnology (now Nature Biotechnology ) and the associated silver detection method (Bassam et al, 1991; Anal. Biochemistry ). We utilized the methodology in a large range of population analyses and map-based cloning approaches. I presented seminars, acted as expert witness and consultant to various national and international agencies (including the United Nations, The International Atomic Energy Agency, General Foods, and the FAO). My overall contribution to the field of plant developmental genetics has permitted others to advance the field sufficiently to permit directed manipulation of the process. Plant mutagenesis and subsequent positional cloning have become the main approach of analysis compared to broad collection of descriptive data. Because of my work the field of plant genetic analysis of legume nodulation has reached a new level of depth. Our recent work on the cloning of the GmNARK receptor kinase from soybean also presents a trend setting achievement as it demonstrates that larger genome crop plants can be used as experimental material to yield information and insights that normally stem from model organisms. Our advances in arbitrary primer technology have helped biomedical as well as plant research. Arbitrary primer PCR is used for the construction of genetic maps, identity testing, as well as RNA expression profiling (e.g., Differential Display). Silver staining is used extensively around the world for microsatellite analysis especially in hospital or teaching environments where other chemicals or radioactivity are undesired. Statement of leadership ability to build world-class research capacity I have demonstrated scientific leadership both intellectually and academically. My academic and creative leadership is illustrated by the large number of graduate students and postdoctoral researchers, as well as sabbatical and research visitors that have prospered from the association with research topics developed by myself. I also see myself as a teacher and have taught genetics and plant developmental biology extensively at the three major universities. I continue to get excellent responses from such undergraduates and even high school students and pride myself for having 'fanned" the interest in my field in so many young minds. I see the combination of researcher and teacher as an important axis for an academic. I want to support my leadership capabilities with three examples: 1) ANU Botany Genetics Group (1979-1988). I was a Research fellow in RSBS working with late Prof. William Hayes, when the opportunity to become a Senior Lecturer in Botany arose. I developed quickly a research focus dealing with the analysis of nodulation and nitrogen fixation. We established good contacts and collaborations with CSIRO Plant Industry and the RSBS efforts. New laboratories were developed and new technologies were introduced. By 1998 I had signed (together with John Shine and Barry Rolfe) a sponsored research contract with the American biotechnology firm Agrigenetics for $2.2 million. This led to the establishment of the Legume Genomics effort in the Botany Department at ANU. We became a vibrant group of international status, attracting international visitors such as Prof. D. Werner, Dr R. Hodson and Prof. J. Beringer. A large number of graduate students, including those co-supervised predominantly with Jim Peacock's group at CSIRO (e.g., Allan Green, Mick Graham, John Evans, Ed Newbingin, Jan Grant) developed as outstanding scientists that now continue the research paradigm and attitude towards discovery in Australian and overseas laboratories. Subsequent to the Agrigenetics funding, I obtained novel Federal government funding through a Section 39 grant ($1.1 million; shared with Barry Rolfe, ANU) to continue the commercialization of the newly discovered supernodulation mutants. I believe that in the 1981-1988 period my laboratory was the most research-intensive and best-funded laboratory in the Faculties Section of the ANU. 2) Racheff Chair of Excellence ( University of Tennessee , USA ). In 1988, despite continued funding from Section 39, I took up the endowed Racheff Chair of Excellence at the University of Tennessee in Knoxville , Tennessee , USA . The Chair was supported by policies of the then Governor Lamar Alexander. I transferred part of the ANU group to UT and established a major research laboratory at the University of Tennessee . We introduced genomic research to the region and acted as a reference centre not only for soybean (grower and other support) but also DNA profiling, based on our newly invented and patented DAF technology. In collaboration with other scientists at UT (Gary Stacey, Beth Mullins, Fred Allen, and Dan Roberts) we established the low funded Centre of Legume Research. As such we build on the strength of the units and became an internationally recognized research focus for nodulation and nitrogen fixation research. We organized the International Congress of Nitrogen Fixation in 1990. This book is still deemed as important and current. We developed Gordon Research Conference like meetings in the 'hills' as the Gatlinburg Symposia that attracted national and international speakers. This developed a strong class of graduate students and postdoctoral fellows. Many of them have now populated US, European and Australian science. These include Brant Bassam, Tara Sutherland, John Culpepper, Noel Geharty, Roel Funke, Shane Abbitt, James Bond, Ray McDonnell, Sanjeev Pillai, Natascha Taranenko, Daci Quan, Ali Ustum, Farshid Ghassemi, to name a few. I left Knoxville in 1999 to return to Australia as a life style and academic decision. 3) University of Queensland In 1999 I returned to UQ to take up the Chair of Botany. I did so because of the excellence of the existing Botany Department, ranging from ecological to molecular research and teaching. I build a major laboratory focusing on the genetics and genomics of legumes. We progressed with the positional cloning of the supernodulation gene through collaboration with Dr B. Carroll's laboratory (a former student and postdoctoral fellow) and interaction with the Australian Genome Research Facility. The laboratory quickly attracted Honours and graduate students, the first of which have recently completed their degrees. International leadership was retained as new staff joined the group and new collaborations were established. The major advance occurred through the successful application for an ARC Centre of Excellence in 2002. This required a complex interaction of the 4 research nodes and the 11 CIs. This was accomplished through open dialogue and a common vision. I believe it was my focus on the understanding of the meristems and their interaction that created the cohesion that pushed the Centre application forward. This cohesion continues today and is expressed at quarterly meetings and the level of seamless scientific interactions within the Centre. More importantly, our research focus is 'right on track' as evidenced by a recent statement of Elliot Meyerowitz (PAG2004) that long distance signaling and the reception of such signal as well as the recognition of gene interactions are the major focus of plant biology. I feel proud to have placed the ARC Centre on that course and see it as an extension of my lifelong ambition to understand more about development in plants, indeed all living forms. I plan to expand the focus of the existing ARC CoE program to look at the biochemical nature of signals and protein interactors. Three postdoctoral appointments in protein biochemistry and structural biology will support the genetics, proteomics, transcriptomics and genomics effort of the Centre. Graduate students will team up with postdoctoral staff to explore key components of phytochemistry. I foresee joint supervision with staff members from the Chemistry and Biochemistry Departments and the IMB. Other evidence of impact on, and major contributions to the fieldI have served my discipline extensively through the organization of two international congresses (Molecular Plant Microbe Interactions, and the International Congress of Nitrogen Fixation). I have written several books and monographs and wrote over 300 reviewed publication receiving more than 5,000 citations. Ten publications have reached the 'century mark' in citation. I contributed, by invitation, to Prof. S. Brenner's Encyclopedia of Genetics (2002). I have contributed to the human resource development of my discipline through teaching, mentoring and supervision. I have supervised and guided a large number of graduate students and post-doctoral fellows. Researchers like David Day, Madelaine Spencer-Borroto, Anwar Hussain, Arno Krotzky, Brant Bassam, Gustavo Caetano-Anolles, Alexander Kolchinsky, Natascha Kruchinina, Jiri Stiller, Dean Price, Bernie Carroll, Manuel Matamoros, Inaki Iturbe-Ormaetxe , Jaime Padilla, Gustavo Gualtieri, Tyrone Ridgeway, Kathy Schuller, David McNeil, Michael Udvardi, Alexander Hansen, Artem Men, Shyam Mohapatra, Angela Delves, and Susan Howitt are among these. Many of these have populated Australian science in positions ranging from Professor to Deputy Vice Chancellor. I have been a regular speaker and contributor to international congresses and have been elected to national academies and learned societies. I have served and still serve on several Editorial boards of key journals in the discipline of plant developmental biology and biotechnology. These include being the editor in chief of the Journal of Plant Physiology for 5 years, and service on the editorial boards of Genome Letters (2001- present), Symbiosis (1994-present), Journal of Biomedicine and Biotechnology (2002-present), Plant Physiology (1989-1992), and Physiologia Plantarum (1992-96). I am particularly proud of the inclusion on the board of Biotechniques , as it contains several Nobel Laureates, and I am the only plant researcher. I have served on international science research review panels, including those for the framework programs of the European Union in Brussels , the British and Japanese governments , the FAO, and UNESCO. These include the Visiting Group for the review of the John Innes Center (Norwich; (BBSRC; April 1997), the review group of British Nitrogen Fixation Research (AFRC: Bath, 1991), the EU's Plant Biotechnology Review Board, Brussels (1992-1997), and being a member of the five person review team of the FAO (United Nations) for the development of a Chilean Government Agricultural Biotechnology Programme (1995). On a personally pleasing note I was an invited member of the prestigious parliamentary delegation to BIO2003 in Washington headed by Queensland Premier Peter Beattie (June 2003). I have contributed through extensive teaching and communication, presenting courses not only in my home universities, but also internationally. For example, I presented lectures on biotechnology and DNA profiling to the National Science School (Australia 1985, 1987), the NATO Summer School (Liege, 1994), the IAEA Molecular Genetics Courses (Seibersdorf, 1990-1996), and in over 325 research seminars. I am a member or Fellow of several Honours and learned societies such as the Russian Academy of Agricultural Sciences (Fellow), the American Association for the Advancement of Science (AAAS; Fellow,) Sigma Xi, Phi Kappa Phi, Phi Beta Kappa, and Gamma Sigma Delta. I review papers regularly for a large range of top journals including Science and Nature . I was nominated for the Australia Science Prize (with W. Broughton and B. Rolfe) in 1998 for our work on the legume nodulation pathway, and received the Phi Kappa Phi National Honors Society Distinguished Scholar Award ( Knoxville , 1993) .
| ||||||||||||||||||||
© COPYRIGHT TO THE AUSTRALIAN PLANT NUTRIOMICS NETWORK | DISCLAIMER/COPYRIGHT | RETURN TO TOP |
||||||||||||||||||||
 |
||||||||||||||||||||