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Molecular Mechanisms of Peroxisome Biogenesis, Function, and Signaling

Peroxisomes are single-membrane-bound organelles that facilitate numerous essential biochemical reactions in nearly all eukaryotic organisms.  The significance of peroxisomes is underscored by the human genetic diseases and the lethal plant phenotypes caused by peroxisomal deficiencies.  Plants have a large number of structurally similar but metabolically specialized peroxisomes that mediate photorespiration, fatty acid β-oxidation, the glyoxylate cycle, nitrogen metabolism, synthesis of plant hormones, and metabolism of hydrogen peroxide.  Recent findings have also revealed a role for peroxisomes in photomorphogenesis and in plant-pathogen interaction. Thus, plant peroxisomes exert their functions in a variety of plant-specific processes bearing agricultural and economical significance.

Figure 1. Plant peroxisomes play diverse roles; their proliferation is regulated by environmental signals such as light and a number of peroxisome proteins, such as the PEX11 family and dynamin-related (DRP) proteins.

Despite their importance, many aspects of peroxisomes are poorly understood. Our laboratory aims to elucidate molecular mechanisms controlling peroxisome biogenesis and to understand how peroxisomes communicate with the environment and other subcellular organelles. We employ a combination of molecular genetic, cell biological, biochemical, genomic, and proteomic approaches and use Arabidopsis as a model system. We train students and postdocs from diverse backgrounds of biology. Current research projects in the laboratory include the following:

(1) Molecular machinery and light control of peroxisome proliferation.

Peroxisomes are highly dynamic and versatile. Various environmental, metabolic, and developmental cues affect the number and size of peroxisomes. The lack of apparent homologs to most proteins that operate in yeast and mammals to control peroxisome proliferation suggests that it is essential to study this fundamental cell biological process in plants. Forward and reverse genetic and molecular approaches have been taken in our lab to identify nuclear and peroxisomal proteins that control this process, especially those involved in the light induction of peroxisome proliferation.

(2) Regulation of peroxisome function by a novel proteolytic pathway.

The ubiquitin-proteasome pathway is an important regulatory mechanism governing many aspects of cell function. We have discovered several novel proteins targeted to the peroxisome that are putatively involved in this pathway. Experiments are underway to determine the targets of this system.

3) Understanding peroxisomal protein networks (an Arabidopsis 2010 project)

Peroxisomes play essential roles in plant development and during plant responses to biotic and abiotic stresses. They are also “organelles at the crossroads” given that different cell compartments are often linked via peroxisomal functions. However, our knowledge of the protein composition and metabolic and regulatory networks within the peroxisome is far from complete. This project aims to discover new peroxisomal proteins and to integrate in silico, proteomics, cell biological, and reverse genetics data into biochemical and regulatory networks within peroxisomes.

Publications

Hu J, Desai M (2008). Light control of peroxisome proliferation during Arabidopsis photomorphogenesis. Plant Signal Behav 3(10). Published online: Abstract

Desai M, Hu J (2008) Light induces peroxisome proliferation in Arabidopsis seedlings through the photoreceptor phytochrome A, the transcription factor HY5 HOMOLOG, and the peroxisomal protein PEROXIN11b. Plant Physiol 146: 1117-1127 Abstract

Hu J (2007) Plant peroxisome multiplication: highly regulated and still enigmatic (invited review). J Int Plant Biol 49(8): 1112-1118  Full Text

Hu J (2007) Toward understanding plant peroxisome proliferation (invited addendum). Plant Signal Behav 2(4): 308-310  Abstract

Orth T, Reumann S, Zhang X, Fan J, Wenzel D, Quan S, Hu J (2007) The PEROXIN11 protein family controls peroxisome proliferation in Arabidopsis. Plant Cell 19: 333-350. Full Text

Fan J, Quan S, Orth T, Awai C, Chory J, Hu J (2005) The Arabidopsis PEX12 gene is required for peroxisome biogenesis and is essential for development. Plant Physiol 139: 231-239.  Full Text

Hu J, Aguirre M, Peto C, Alonso J, Ecker J, Chory J (2002) A role for peroxisomes in photomorphogenesis and development of Arabidopsis. Science 297: 405-409.  Full Text

Yin Y, Cheong H, Friedrichsen D, Zhao Y, Hu J, Mora-Garcia S, Chory J (2002) A crucial role for the putative Arabidopsis topoisomerase VI in plant growth and development. Proc Natl Acad Sci U S A 99: 10191-10196.  Full Text

Hu J, Reddy VS, Wessler SR (2000) The rice R gene family: two distinct subfamilies containing several miniature inverted-repeat transposable elements. Plant Mol Biol 42: 667-678. Full Text

Hu J, Anderson B, Wessler SR (1996) Isolation and characterization of rice R genes: evidence for distinct evolutionary paths in rice and maize. Genetics 142: 1021-1031.   Full Text

Teaching

(1) PLB865, Plant Growth and Development

Offered in the fall of alternate years to graduate students; 3 credits.

Course description: Genetics and biochemistry of development in higher plants as influenced by genes and environment. Biosynthesis, action and signal transduction of phytohormones and other signaling molecules. Patterning, meristem organization and formation of tissues and organs. Genetic mechanisms underlying developmental diversity.

(2) PLB499, Senior Seminar

Offered in the spring of each year to senior plant biology majors; 2 credits.

Course description: Current issues in plant biology. Scientific writing and oral presentation.

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