Research: Dr. Lawrence J. Hobbie

Our research focuses on plant developmental genetics. We are interested in identifying and understanding the function of genes that control plant growth and development, particularly those that act through the important plant hormone auxin. We are working with single-gene mutants of the model plant Arabidopsis thaliana that have abnormal responses to auxin; through physiological, genetic, and molecular characterization of theses plants, we hope to gain a better understanding of exactly what auxin does and how it does it.

What I study: Introduction to the plant hormone auxin

We are interested in how the growth and development of plants is controlled. This is obviously too big a question for one lab to answer! We have chosen to focus on a small part of this large problem, namely, how does the plant hormone auxin work, and what does it do?

Auxin is a small molecule that has been intensively studied for over 70 years because of its importance in plant growth and development. The major naturally occurring form of auxin is indole-3-acetic acid, or IAA, but a wide variety of synthetic compounds that behave like auxins when applied to plants have also been identified and are widely used, including naphthalene acetic acid (NAA) and 2,4-D (dichlorophenoxyacetic acid).

Roles of auxin in plants

Auxin is important for plants’ responses to light and gravity, for the formation and elongation of lateral roots and shoots, for the formation of vascular tissue, and for embryonic development. If a shoot is illuminated from one side, for example, the shoot bends towards the light; this process is believed to depend on auxin, which accumulates on the shaded side of the shoot and causes the cells on that side to elongate more than those on the side close to the light, thereby causing the shoot to bend. Auxin’s role in these processes at the whole plant level results from its effects at the cellular level, including cell elongation, cell division, and cell differentiation. Its effects in a particular case depend on its concentration and the type and state of the tissue.

Auxin signal transduction

We are interested in knowing how auxin produces its effects: what are the biochemical reactions that lead from the signal received by a cell (auxin) to the changes in the cell that result in elongation, division, or differentiation? This series of biochemical reactions is called the signal transduction pathway. Our past research on the genes AUXIN-RESISTANT5 and AUXIN-RESISTANT6 dealt with auxin signal transduction.

Auxin transport

Auxin is the only plant hormone that is known to be transported within plants. Auxin can move through the phloem along with sugars and other substances, but the best-characterized mode of auxin transport is the polar auxin transport pathway. In this pathway, auxin enters cells either by diffusion or by active uptake through auxin import proteins, and then exits cells down an electrochemical gradient through polarly-localized auxin efflux carriers which provide directionality to auxin movement. Three classes of auxin transport proteins have been identified: the AUX1/LAX family of auxin importers, the PIN family of auxin effluxers, and the MDR/PGP family of ATPase transporters which may function in both import and efflux. Recently my lab has been concentrating on a protein that appears to be important for auxin influx, the AUXIN-RESISTANT4 protein.

How do we study these topics?

Introduction to the use of genetics and molecular biology for the analysis of biological problems

The approach that we and others are taking to figure out how auxin works is called a genetic and molecular biological approach. Such an approach has been very important in many of the key advances in modern biology.

Use of Arabidopsis in research on plants

One key to the success of the genetic and molecular biological approach is using the right organism. We have chosen a particular plant to work on because it has many advantages for laboratory research. The plant is called Arabidopsis thaliana, or Arabidopsis for short. Its common name is wall cress or mouse-ear cress; it is a relative of broccoli and mustard, but is itself not economically important or tasty. It is being used around the world to study basic questions in plant biology. It is small and grows fast, so laboratory studies can be done rapidly and conveniently. In addition, it turns out to be relatively easy to clone genes in Arabidopsis because it has less "junk DNA" than most other plants. Once genes have been cloned and processes understood in Arabidopsis, the knowledge gained is almost always applicable to most other plants. Once a gene for an important enzyme has been cloned in Arabidopsis, for example, it can be cloned easily from other plants that are more commercially important but more difficult to study. Thus, Arabidopsis has become a "model system" for plant research. Indeed, it is so widely studied, and viewed as so important, that it was the first plant to have its entire genome sequence determined, in the year 2000. You can follow this link to the Arabidopsis database, which collects information about many aspects of Arabidopsis research.

Identification of mutants with altered responses to auxin

So, how have we and others applied the genetic and molecular biological approach to understand how auxin works? First, we needed to identify mutants that may have a defect in auxin signal transduction or auxin transport. To do so, we used the observation that high concentrations of auxin will inhibit the growth of plants; in fact, synthetic versions of auxin such as 2,4-D have been widely used as herbicides. Thus, if we grow normal plants on high concentrations of auxin, they will be stunted, with very short roots and other morphological abnormalities. However, plants with defects in some aspect of auxin physiology would not transport, detect, or respond to the high concentrations of auxin, and would grow more normally. These plants are called auxin-resistant or auxin-insensitive. It is very easy to identify such auxin-resistant plants.

We and others have isolated a number of auxin-resistant mutants of Arabidopsis by taking mutagenized Arabidopsis seeds, sterilizing them, and plating them on plates of nutrient agar containing auxin. At the concentration used, wild-type (normal) plants did not elongate roots, but some mutants that could elongate roots were found. These have been characterized and found to define a number of different genes. Some of the mutants are called aux1, axr1 (for "auxin-resistant 1"), axr2 etc. up to axr6. Other labs, including the lab of Dr. Mark Estelle, then at Indiana University (now at UCSD), where I trained as a post-doctoral fellow, have characterized many of these mutants. We have characterized the physiology and development of these mutants with the goal of understanding the function of the genes in the normal life of the plants, and have used the mutations as "tags" to clone the genes, with the goal of determining the biochemical function of the proteins. Mutations and genes that our lab has characterized in the past include AXR5 (see paper by Yang et al., 2003) and AXR6 (see papers by Hobbie et al., 2000, and Hellmann et al., 2003).

Current research in my lab:

Characterization of genetic modifiers of axr4

The main focus of work in our laboratory at the moment is characterizing genetic modifiers of a gene called AXR4. I isolated and studied the axr4 mutants as a post-doctoral fellow at Indiana University (Hobbie and Estelle, 1995). The AXR4 gene was subsequently cloned by Sunethra Dharmasiri and colleagues in the Estelle lab at Indiana, and additional characterization of the mutant was carried out by Ranjan Swarup in the lab of Malcolm Bennett at Nottingham University in England. Their results (Dharmasiri et al., 2006) show that the AXR4 gene is essential for the proper localization of the auxin import carrier AUX1. However, the sequence of the AXR4 protein did not reveal its function. We are trying to discover the molecular function of AXR4, and identify other components of plant cells necessary for proper polar localization of proteins, using a genetic approach. We have identified a large number of additional mutations that either enhance or suppress the effects of the axr4 mutation on auxin-responsive root elongation. We are currently characterizing these enhancer and suppressor mutations. To support this research, I was awarded a 3-year $350,000 grant from the National Science Foundation for the period 2005-2008 (extended without additional funds to 2009).

Lab facilities

We carry out our research in a large lab in the basement of the Science Building on Adelphi’s Garden City campus. This lab was renovated during summer 2006; here’s a photo of the new lab.

Laminar flow hoods (“sterile hoods”), refrigerators, freezers, and gel imaging equipment is in an adjacent room. A separate air-conditioned room equipped with racks and lights is used for growing our plants. Other necessary equipment is available elsewhere in the department.

Student research in my lab

Undergraduates and master’s students who do research in the lab learn techniques of genetic, physiological, and molecular biological analysis. Over the past fifteen years numerous students have done research with me; many of the undergraduates have presented their work at scientific conferences and have submitted their work as a senior thesis and/or for Honors in Biology. Master’s students who have completed their degrees with me have entered Ph.D programs at Queens College, St. John’s University, Stony Brook University, and Iowa State University, or have found employment in industry and government labs in the pharmaceutical, life sciences, and forensics sectors. Recent master’s student graduates from my lab include Ms. Ogechukwu Eze, currently a student at Yale Medical School, Mr. David Chau, currently a student at the University of Houston College of Optometry, Mr. Francis Onwochei, a student at the St. George’s School of Medicine, and Ms. Achala Jayasena, a student in the plant pathology Ph.D program at Iowa State University. This photo shows the summer 2008 Hobbie lab:

From left, back row: Dr. Hobbie, Patricia Raimondi, David Chau, Michael Auricchio, Achala Jayasena, Nitasha Dhiman; front row: Pauline Gould, Dory Londono.

My students regularly make presentations at scientific conferences. In 2008, Achala Jayasena presented a poster at the International Conference on Arabidopsis Research in Montreal. On June 2, 2007, Oge gave a talk at the NY Area Plant Molecular Biology Meeting, held in New Haven, Connecticut on June 2. In 2002, three students presented posters and one gave a talk at the meeting of the Northeast regional section of the American Society of Plant Biology, held at Wellesley College on May 4-5 (the picture shows Jane Jaroonnarm (now a graduate of Tufts Dental School), Kimberly Kranz (now a graduate of Stony Brook Medical School), master's student Sungsu Lee (who entered the Ph.D program in biology at St. John’s University), and Harleen Kaur (now a graduate of Tufts Dental School) in front of their posters at the conference).

Interested in working in my lab?

Please note that due to limits on space in the lab and the time and energy available for supervision of students, I am unable to accept high school students into my lab. Ms. Pauline Gould, our lab technician, and I take pleasure in supervising undergraduate and master’s student researchers in the lab, for credit or on a volunteer basis, during the school year and over the summer. Acceptance into my lab requires some background in biology, preferably including genetics, along with a commitment to work at least 6 hours a week with diligence and intelligence for at least two semesters. Acceptance into the lab is based on a student’s academic record and a personal interview. Be aware that research is a serious commitment: it will require both mental and physical involvement, and a considerable number of hours per week, to do a good job.

Students who join my lab are assigned a project based on the current research needs of the lab and their interests, after discussion with me. Students are trained in lab safety and necessary techniques; students begin work under supervision, but are given increasing independence as they master skills. Students are expected to keep meticulous notes of their experiments, attend lab meetings and participate in lab chores.

Selected References

Dharmasiri, S., Swarup, R., Mockaitis, K., Dharmasiri, N., Singh, S.K., Kowalchyk, M., Marchant, A., Mills, S., Sandberg, G., Bennett, M.J., and Estelle, M. 2006. “AXR4 is required for localization of the auxin influx facilitator AUX1.” Science 312: 1218-1220.

Hellmann, H., Hobbie, L., Chapman, A., Dharmasiri, S., Dharmasiri, N., del Pozo, C., Reinhardt, D., and Estelle, M. 2003. “Arabidopsis AXR6 encodes CUL1 implicating SCF E3 ligases in auxin regulation of embryogenesis.”

EMBO Journal 22: 3314-3325.

Hobbie, L., and Estelle, M. 1995. "The axr4 auxin-resistant mutants of Arabidopsis define a gene important for root gravitropism and lateral root initiation." The Plant Journal 7: 211-220.

Hobbie, L., McGovern, M., Hurwitz, L.R., Pierro, A., Liu, N.Y., Bandyopadhyay, A., and Estelle, M. 2000. "The axr6 mutants of Arabidopsis define a gene involved in auxin response and early development." Development 127: 23-32.

Hobbie, L.J. 1998. "Auxin: molecular genetic approaches in Arabidopsis." Plant Physiology & Biochemistry, 36: 91-102.

Hobbie, L.J. 2006. “Auxin and cell polarity: the emergence of AXR4.” Trends in Plant Science 11: 517-518.

Ruegger, M., Dewey, E., Gray, W.M., Hobbie, L., Turner, J., and Estelle, M. 1998. "The TIR1 protein of Arabidopsis functions in auxin response and is related to human SKP2 and yeast Grr1p." Genes & Development, 12: 198-207.

Ruegger, M., Dewey, E., Hobbie, L., Brown, D., Bernasconi, P., Turner, J., Muday, G., and Estelle, M. 1997. "Reduced NPA-binding in the tir3 mutant of Arabidopsis is associated with a reduction in polar auxin transport and diverse morphological effects." Plant Cell 9: 745-757.

Yang, X., Lee, S., So, J.H., Dharmasiri, S., Dharmasiri, N., Ge, L., Jensen, C., Hangarter, R., Hobbie, L., and Estelle, M. 2004. “The IAA1 protein is encoded by AXR5 and is a substrate of SCF(TIR1).” Plant Journal, 40: 772-782.