The Groups > Professor Jim Whelan
 

Associate Professor Jim Whelan
Associate Professor
Plant Molecular Biology
School of Biomedical and Life Sciences
The University of Western Australia

Website Address: http://www.mitoz.bcs.uwa.edu.au/
Email: seamus@cyllene.uwa.edu.au

Research Aims
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The Big Question

How and When Do Plants Make Mitochondria?

The Short-Term Goals

  • To Elucidate the Signals that Initiate Mitochondrial Biogenesis in Plants.
  • To Characterise the Apparatus Responsible for Protein Import into Mitochondria
  • To Uncover the Signals and Mechanism Involved in Inter-organelle Communication in Plants.

Molecular Biology

DNA and RNA purification, cDNA and genomic gene identification using a variety of screening methods, Gene expression analysis using Northern and real-time PCR, Southern and Western blot analysis, Site directed mutagenesis, Protein expression, DNA sequencing, Various PCR technologies including competitive PCR, inverse PCR and real time PCR. Microarray analysis of gene expression.

Molecular Genetics

Yeast molecular genetics, cDNA subtractive hybridisation, Promoter analysis using a variety of transgenic systems with various marker genes. Promoter and Enhancer trap screens in Plants.

Cell Biology

Protein targeting, Confocal microscopy, GFP as a marker protein, Protein uptake assay into organelles, Signal transduction in plants.

Research Interests

The primary focus of my research laboratory is on mitochondrial biogenesis in plants. We investigate how plants make mitochondria and how this changes and differs between tissues and with development. We use a variety of approaches to understand this process:

  1. Characterisation of changes in various mitochondria activities and how they change in different tissues and with development.
  2. Analysis of nuclear and mitochondrial gene expression.
  3. Characterisation of the signals and pathways responsible for inducing mitochondrial gene expression.
  4. Protein import and targeting studies.
  5. Cell biology approaches to assess mitochondrial numbers and proteins.
  6. Analyse knock-out plants for various mitochondrial components to determine affects on mitochondrial biogenesis and various signalling pathways affecting mitochondrial proteins.

These approaches are use in combination so as an overall picture of mitochondrial biogenesis is achieved - see http://www.mitoz.bcs.uwa.edu.au/

Research Aims
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Group (Laboratory) Members (and areas of research)

Tamzin Donald - Promoter analysis using trapping technologies

Monika Murcha - Characterisation of Mitochondrial protein Import pathways

Orinda Chew - Characterisation of dual targeting pathways and signals/Inter-organelle communication

May-Nee Lee - Mitochondrial protein Import and analysis of import components using knock-out plants

Dave Thirkettle-Watts - Characterisation of promoters controlling nuclear encoded mitochondrial gene expression for respiratory chain proteins

Rachel Clifton - i) Characterisation of promoters controlling nuclear encoded mitochondrial gene expression for respiratory chain proteins
ii) Characterisation of global gene expression using Microarray approaches.

Ryan Lister - i) Characterisation of promoters controlling nuclear encoded mitochondrial gene expression for protein import components
II) Characterisation of global gene expression using Microarray approaches.

Kate Howell - Characterisation of gene expression of nuclear encoded genes for mitochondrial proteins using Rice as a model.

Dina Elhfaz - Characterisation of alternative NADH dehydrogenases in plants

Lois Ho - Characterisation of promoters controlling nuclear encoded mitochondrial gene expression for respiratory chain proteins

Adam Carroll - Characterisation of sub-cellular localisation of mRNA in plant cells

Kathryn Holt - Analysis of Microarray expression data

Daniela Sabbioni - Characterisation of promoters controlling nuclear encoded mitochondrial gene expression for protein import components

Amy Capobianco - Characterisation of promoters controlling nuclear encoded mitochondrial gene expression for respiratory chain proteins

Funding

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Current

  • Functional Genomics of Plant Mitochondria: Their Role in Development, Oxidative Stress and Plant Defense (with Day, Millar and Singh)(ARC Discovery 2002-2006 ~$500,000 per year)
  • Genome Approaches to Investigate Metabolic Coordination in Plant Cells
    ( with atkins and smith ) (ARC Discovery 2003-2005 ~ $120,000 per year)

Applications submitted or planned

Techniques in the Laboratory
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Currently active
  • Analysis of gene expression using i) Real-Time PCR and ii) Microarray
  • Characterisation of promoters regions using transgenic approaches
  • Organelle isolation and uptake assays of expressed protein
  • Protein expression
  • Yeast as a model organism to elucidate the function of plant genes

In development

  • •Promoter analysis using trapping approaches
  • Identification of transcription factors using affinity purification and mass spectrometry
  • Gene expression from single cells
Main areas of expertise
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Top three areas of knowledge
  1. Protein import into mitochondria
  2. Control of nuclear encoded genes encoding mitochondrial (+ organelle) proteins
  3. Signalling and Retrograde pathways controlling gene expression

Top three technical skills

  1. Analysis of gene expression using Real-Time PCR and Microarray analysis
  2. Deletion analysis of promoter regions to identify functional motifs
  3. Protein uptake assays into organelles
A statement on your most significant contributions to this research field
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  • I have been involved in the field of plant molecular biology research for over 15 years and believe that I have made the following significant findings:

  • I developed and carried out the first protein import experiments into plant mitochondria, and investigated sorting from chloroplasts in homologous systems. This methodology is widely used and cited by other workers in plant mitochondrial import/biogenesis field. More recently I have developed methodology to specifically study dual targeting to mitochondria and plastids, an article that was listed in the F1000 which indicates its importance in this field. I have identified several dual targeted proteins and demonstrated that they are stress regulated.

  • I have characterised several different import pathways into plant mitochondria, and shown that they may be regulated differently by tissue, developmental and diurnal controls. Recently I have shown that mitochondrial protein import is stress regulated and have demonstrated using whole genome transcriptomics that this is due to global changes in gene encoding components of the mitochondrial protein import apparatus, morphology and division.

  • I have studied mitochondrial gene expression, with particular emphasis to respiratory gene expression, elucidating that members of multi-families are expressed in a developmental and tissue specific manner. I have been involved in analysing how stress affects genes expression and have characterised both positive and negative regions in promoters which are responsible for stress related gene expression.

  • I have carried out studies on the nature of gene transfer from the mitochondrion to the nucleus using examples of gene transfers that occur frequently as seen with several mitochondrial ribosomal proteins and rare transfers such as that of subunit 2 of cytochrome c oxidase that has only occurred once in higher plants.

In conclusion I believe that my contribution to the field has been significant as evidenced by my publication record and that the studies I have carried out are broad ranging and have importance in understanding mitochondrial biogenesis and mitochondrial responses to stress.

Other evidence of impact and contributions to the field
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I believe that my contribution to the field of plant mitochondrial research is internationally recognised as evidenced by the following:

  • I have received several fellowships to travel to carry out collaborative research, from the OECD, the Werner-Gren Foundation and Swedish Research Council to carry out collaborative studies with Prof E. Glaser, at the Biochemistry Department, Stockholm University . Most recently in 2001 I have received an Alexander Von Humboldt research fellowship to carry out collaborative studies with Prof E. Pratje, Botany Department , Hamburg University.

  • In 1998 I was awarded the Australian Society of Plant Physiology Goldacre award for research excellence.

  • I have developed several national and international collaborations. As well as those mentioned above I have collaborations with Dr. Susan Howitt ANU, Dr Barry Pogson ANU, Dr Michael Uvardi, Max-Plank Golm, Associate Prof Kinyma Toriyama, Sendi University (funded for sabbatical and return visit to my laboratory by Japanese and Australian Academy of Sciences) and Prof Jeff Palmer, Indiana University .

  • I review papers for Plant cell, Plant Physiology, Plant Journal, Plant Molecular Biology, Plant Biology, Journal of Plant Physiology, Plant Science, Journal of Molecular Biology, Molecular Evolution and the I am a section editor (molecular biology) for Plant Biology.

I have been invited with colleagues to edit a volume of the prestigious series "Advances in Photosynthesis and Respiration" by Kluwer publishers and I am currently writing with colleagues a chapter entitled "Mitochondrial Biogenesis and Function" for the Arabidopsis book on line at http://aspb.org/publications/arabidopsis/ .

All refereed publications in the past five years
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Book Chapters

  • Howell, K.A., Lister, R. Whelan, J. (2004). Expression analysis of mitochondrial components in a variety of plant species using Real-Time Quantitative PCR. In: Rapid Cycle Real-Time PCR - methods and applications. Wittwer, C., Hahn, M. Kaul, K (eds). Springer-Verlag , Berlin Heidelberg .

  • Millar, A.H., Day, D.A., Whelan, J. (2004). Mitochondrial biogenesis and function in Arabidopsis. In The Arabidopsis Book, eds. C.R. Somerville and E.M. Meyerowitz, American Society of Plant Biologists, Rockville, MD, doi/10.1199/tab.0009, http://www.aspb.org/publications/arabidopsis/

Invited Reviews

  • Heazlewood, J.L., Millar, A.H., Day, D.A., Whelan, J. (2003). What makes a mitochondrion. Genome Biology 4: 218-211.

  • Millar, H., Considine, M.J., Day, D.A., Whelan, J. (2001). Unravelling the role of mitochondria during oxidative stress in plants. IUBMB Life 51: 201-205.

  • McCabe, T.M., Daley, D.O., Whelan, J. (2000). Regulatory, Developmental and Tissue Aspects of Mitochondrial Biogenesis in Plants. Plant Biology 2: 121-135.

  • Whelan, J. (1999). Control of protein import into plant mitochondria. (Goldacre Review) Australian Journal of Plant Physiology 26: 725-732.

Research Papers

  • Lister, R., Chew, O., Lee, M-N, Heazlewood, J.L., Clifton , R., Parker, K.L., Millar, A.H., Whelan, J. (2004). A transcriptomic and proteomic characterisation of the Arabidopsis mitochondrial protein import apparatus and its response to mitochondrial dysfunction. Plant Physiol 134: 777-789.

  • Chew, O., Lister, R., Qbabou, S., Heazlewood, J.L., Soll, J., Schleiff, E., Millar, A.H., Whelan, J. (2004). A plant outer mitochondrial mem,brane protein with high amino acid sequence identity to a chloroplast protein import receptor. FEBS lett 557: 109-114.

  • Norman, C., Howell, K.A., Millar, A.H., Whelan, J., Day, D.A. (2004). Salicylic acid is an uncoupler and inhibitor of mitochondrial electron transport. Plant Physiol 134: 492-501.

  • Heazlewood, J.L., Tonti-Filipini, J., Gout, A. M., Day, D.A., Whelan, J., Millar, A.H. (2004). Experimental analysis of the Arabidopsis mitochondrial proteome highlights signalling and regulatory components, provides assessments of targeting prediction programs, and indicates plant-specific mitochondrial proteins. Plant Cell 16: 241-256.

  • Moore , C.S., Cook-Johnson, R., Rudhe, C., Whelan, J ., Day, D.A., Wiskich, J.T., Soole, K.L. (2003). Identification of AtNDI1, an internal non-phosphorylating NAD(P)H dehydrogenase in Arabidopsis thaliana mitochondria. Plant Physiology 133: 1968-1978.

  • Thirkettle-Watts, D. Mccabe, T.C., Clifton , R., Moore , C., Finnegan, P.M., Day, D.A., Whelan, J. (2003). Analysis of alternative oxidase promoters from soybean. Plant Physiology 133: 1158-1169.

  • Qualmann, S.R., Daley, D.O., Whelan, J., Pratje, E. (2003). Import pathway of nuclear-encoded cytochrome oxidase subunit 2 using yeast as a model. Plant Biology 5: 481-490.

  • Chew, O., Rudhe, C., Glaser, E., Whelan, J. (2003). Characterisation of the targeting signal of dual-targeted pea glutathione reductase. Plant Molecular Biology 53: 341-356.

  • Chew, O., Whelan, J., Millar, A.H. (2003). Molecular definition of the ascorbate-glutathione cycle in Arabidopsis mitochondria reveals dual targeting of antioxidant defenses in plants. Journal of Biological Chemistry 278: 46869-46877.

  • Holtzapffel, R.C., Castelli, J., Finnegan, P.M., Millar, A.H., Whelan, J., Day, D.A. (2003). A tomato alternative oxidase protein with altered regulatory properties. Biochimica et Biophysica Acta 1606: 153-162.

  • Chew, O. and Whelan, J. (2003). Dual targeting ability of targeting signals is dependent on the nature of the mature protein. Functional Plant Biology 30: 805-812.

  • Taylor , N.L., Rudhe, C., Hulett, J.M., Lithgow, T., Glaser, E., Day, D.A., Millar, A.H., Whelan, J. (2003). Environmental stresses inhibit and stimulate different protein import pathways in plant mitochondria. FEBS letters 547: 125-130.

  • Considine, M.J., Goodman, M., Echtay, K.S., Laloi, M., Whelan , J., Brand, M.D., Sweetlove, J. (2003). Superoxide stimulates a proton leak in potato mitochondria that is related to the activity of uncoupling protein. Journal of Biological Chemistry 278: 22298-22302.

  • Heazlewood, J.L., Howell, K.A., Whelan, J. and Millar, A.H.M. (2003). Towards the analysis of a rice mitochondrial proteome. Plant Physiology 132: 230-242.

  • Heazlewood, J.L., Whelan, J. and Millar, A.H.M. (2003). The products of mitochondrial orf25 and orfB are Fo components in the plant F1Fo ATPsynthase. FEBS lett 540: 201-205.

  • Murcha, M.W., Lister, R., Ho, A.Y.Y., Whelan, J., (2003). Identification, expression and import of translocase of the inner membrane components 17 and 23 from Arabidopsis thaliana . Plant Physiology 131: 1737-1747.

  • Dessi, P., Pavlov, P.F., Walberg, F., Rudhe, C., Brack, S. Whelan, J., Glaser, E., (2003). Investigations on the in vitro ability of mitochondrial precursor proteins synthesised in wheat germ transcription-translation extract. Plant Molecular Biology 52: 259-271.

  • Daley, D.O., Considine, M.J., Howell, K.A., Millar, A.H., Day, D.A., Whelan, J . (2003). Respiratory gene expression in soybean cotyledons during post-germinative development. Plant Molecular Biology 51: 745-755.

  • Lister, R., Murcha, M.W., Whelan, J . (2003). The mitochondrial protein import machinery of plants (MPIMP) database. Nucleic Acids Research 31: 325-327.

  • Rudhe, C. Clifton, R., Whelan, J., Glaser, E. (2002). N-terminal domain of the dual targeted pea glutathione reductase signal peptide controls organellar targeting efficiency. Journal of Molecular Biology 324: 577-585.

  • Daley, D.O., Clifton , R., Whelan, J. (2002). Gene transfer of cox2 in legumes required changes in specific amino acids to reduce local hydrophobicity and allow import. Proceedings of the National Academy of Sciences ( USA ) 99: 10510-10515.

  • Djajanegara, I. , Finnegan, P.M., Mathieu, C., McCabe, T., Whelan, J., Day, D.A. (2002). Regulation of alternative oxidase gene expression in soybean. Plant Molecular Biology 50: 735-742.

  • Considine, M.J., Holtzapffel, R.C., Day, D.A., Whelan, J. , Millar, A.H. (2002). Molecular distinction between alternative oxidase from Monocots and Dicots . Plant Physiology 129: 949-953.

  • Lister, R., Mowday, B., Whelan, J., Millar, A.H. (2002). Zinc-dependent intermembrane space proteins stimulate import of carrier proteins into plant mitochondria. The Plant Journal 30: 555-566.

  • Adams , K.L., Daley, D.O., Whelan, J., Palmer, J.D. (2002). Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterparts. Plant Cell 14: 931-943.

  • Rudhe, C., Chew, O., Whelan, J ., Glaser, E. (2002). A novel in vitro system for simultaneous import of precursor proteins into chloroplasts and mitochondria. The Plant Journal 30: 213-220.

  • Daley, D.O., Adams, K.L., Clifton , R., Qualmann, S., Millar, A.H., Palmer, J.D., Pratje, E., Whelan, J. (2002). Gene transfer from the mitochondrion to the nucleus: Novel mechanisms for gene activation from Cox2. The Plant Journal 30: 11-21.

  • Rissler, H.M., Collakova, E., DellaPenna, D., Whelan, J., Pogson, B.J. (2002). Chlorophyll Biosynthesis. Expression of a second ChlI gene of magnesium chelatase in Arabidopsis supports only limited chlorophyll synthesis. Plant Physiology 128: 1-10.

  • Shelden, M.C., Dong, B., de Bruxelles, G.L., Trevaskis, B., Whelan, J. Ryan, P.R., Howitt, S.M.., Udvardi, M.K. (2001). Arabidopsis ammonium transporters, AtAMT1;1 and AtAMt1;2, have different biochemical properties and functional roles. Plant and Soil 231: 151-160.

  • Lister, R., Chew, O., Rudhe, C., Lee, M-L., Whelan, J. (2001). Arabidopsis thaliana ferrochelatase-I and -II are not imported into Arabidopsis mitochondria. FEBS letters 506: 291-295.

  • Mehmet, D., Ahmed, F.A., Cummins, J.M., Martin, R., Whelan, J. (2001). Quantitation of the common deletion in human testicular mitochondrial DNA by competitive PCR assay using a chimeric competitor. Molecular Human reproduction 7: 301-306.

  • Ahmed, F.A., Jequier, A.M., Cummins, J.M., Whelan, J . (2001). Differentially expressed DNA sequences following recovery from unilateral testicular torsion in rat. Biochimica et Biophysica Acta 1535: 192-199.

  • Zhang, X.P., Sjoling, S., Tanudji, M., Somogyi, L., Andreu, D., Eriksson, G., Graslund, A., Whelan, J. , Glaser E. Mutagenesis and computer modelling approach to study determinants for recognition of signal peptides by the mitochondrial processing peptidase. The Plant Journal 27: 427-438.

  • Considine, M.J., Daley, D.O., Whelan, J . (2001). The Expression of Alternative Oxidase and Uncoupling Protein during Fruit Ripening in Mango ( Mangifera indica L.). Plant Physiology 126: 1619-1629.

  • Ahmed, F.A., Whelan, J., Jequier, A.M., Cummins, J.M. (2000). Torsion-induced injury in rat testes does not affect mitochondrial respiration or the accumulation of mitochondrial mutations. International Journal of Andrology 23: 347-356.

  • Tanudji, M., Dessi, P. Murcha, M.W., Whelan, J. (2000). Protein import into plant mitochondria. ATP and membrane potential requirements differ between precursor proteins. Plant Molecular Biology 45: 317-325.

  • Adams , K., Daley, D.O., Qiu, Y-L., Whelan, J ., Palmer, J. (2000). Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 408: 354-357.

  • Maasev, D., Newbigin, E., Whelan, J. , Lithgow, T. (2000). How do plant mitochondria avoid importing chloroplast proteins: Tom20 and Tom22 from Arabidopsis thaliana differ from their fungal counterparts. Plant Physiology 123: 811-816.

  • Whelan, J., Smith, M.K., Finnegan, P.M., Day, D.A. (1999). Cloning and sequencing of a genomic clone for the alternative oxidase (Accession No. AF083880) from soybean . Plant Physiology 120: 663.

  • Murcha, M.W., Huang, T., Whelan, J. (1999). Import of precursor proteins into mitochondria from soybean tissues during development. FEBS letters 464: 53-59.

  • Tanudji, M., Djajanegara, I.N., Daley, D.O., McCabe, T.C., Finnegan, P.M., Day, D.A., Whelan, J. (1999). The multiple alternative oxidase proteins of soybean. Australian Journal of Plant Physiology 26: 337-344.

  • Tanudji, M., Sjoling, S. Glaser, E., Whelan, J. (1999). Signals required for the import and processing of the alternative oxidase. The Journal of Biological Chemistry 274: 1286-1293.

  • Ahmed, F., Kougianos, E., Cummins, J.M., Jequier, A.M., Whelan, J . (1999). A Single Step Method for the Determination of the Amount of the Common Deletion in Mitochondrial DNA. Biotechniques 26: 290-300..
Ten career-best publications
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  1. Lister, R., Chew, O., Lee, M-N, Heazlewood, J.L., Clifton , R., Parker, K.L., Millar, A.H., Whelan, J. (2004). A transcriptomic and proteomic characterisation of the Arabidopsis mitochondrial protein import apparatus and its response to mitochondrial dysfunction. Plant Physiology 134: 777-789.

  2. Thirkettle-Watts, D. Mccabe, T.C., Clifton , R., Moore , C., Finnegan, P.M., Day, D.A., Whelan, J. (2003). Analysis of alternative oxidase promoters from soybean. Plant Physiology 133: 1158-1169.

  3. Murcha, M.W., Lister, R., Ho, A.Y.Y., Whelan, J., (2003). Identification, expression and import of translocase of the inner membrane components 17 and 23 from Arabidopsis thaliana . Plant Physiology 131: 1737-1747.

  4. Daley, D.O., Clifton , R., Whelan, J. (2002). Gene transfer of cox2 in legumes required changes in specific amino acids to reduce local hydrophobicity and allow import. Proceedings of the National Academy of Sciences ( USA ) 99: 10510-10515

  5. Daley, D.O., Adams, K.L., Clifton , R., Qualmann, S., Millar, A.H., Palmer, J.D., Pratje, E., Whelan, J. (2002). Gene transfer from the mitochondrion to the nucleus: Novel mechanisms for gene activation from Cox2. The Plant Journal 30: 11-21.

  6. Considine, M.J., Daley, D.O., Whelan, J. (2001). The Expression of Alternative Oxidase and Uncoupling Protein during Fruit Ripening in Mango ( Mangifera indica L.). Plant Physiology 126: 1619-1629.

  7. Adams , K., Daley, D.O., Qiu, Y-L., Whelan, J., Palmer, J. (2000). Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 408: 354-357.

  8. Tanudji, M., Sjoling, S. Glaser, E., Whelan, J. (1999). Signals required for the import and processing of the alternative oxidase. The Journal of Biological Chemistry 274: 1286-1293.

  9. McCabe, T., Finnegan, P.M., Millar, A.H., Day, D.A., Whelan, J. (1998). Control and expression of the alternative oxidase during soybean cotyledon development. Plant Physiol ogy 118: 675-683.

  10. Whelan, J., Knorpp, C. and Glaser, E. (1990). Sorting of precursor proteins between isolated spinach leaf mitochondria and chloroplasts. Plant Molecular Biology 14: 977-982.

 

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