From Genome to Life:Structural, Functional and Evolutionary Approaches

Cargèse, Corsica July 15 - 26, 2002

Hypothetico-deductive science and the function of cytoplasmic genomes

John F. AllenLund University, Sweden, Plant Cell Biology-Plant Biochemistry

http://plantcell.lu.se

Popper, K.R. The Bucket and the Searchlight: Two Theories of Knowledge. Appendix to "Objective Knowledge. An Evolutionary Approach". Oxford University Press, Oxford. 1972.

KARL POPPER

1902-1994

Hypothetico-deductive science(After Popper)

Problem in existing knowledge

Proposed, tentative solution - Hypothesis

Predictions - potential falsifications

- explanations of existing knowledge

- reasons for doing experiments: to test hypotheses

New Problem OR Falsification of hypothesis

Mitochondria and Chloroplasts

From:

Goodsell, D. S. The Machinery of Life. Springer-Verlag, New York and Berlin, 1993

Problem

Why Do Mitochondria and Chloroplasts Have Their Own Genetic Systems?

Why do mitochondria and chloroplasts require their own separate genetic systems when other organelles that share the same cytoplasm, such as peroxisomes and lysosomes, do not? …. The reason for such a costly arrangement is not clear, and the hope that the nucleotide sequences of mitochondrial and chloroplast genomes would provide the answer has proved unfounded. We cannot think of compelling reasons why the proteins made in mitochondria and chloroplasts should be made there rather than in the cytosol.

Molecular Biology of the Cell© 1994 Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D. WatsonMolecular Biology of the Cell, 3rd edn. Garland Publishing

Proposed solutions (hypotheses)

The “Lock-in” hypothesis. (Bogorad, 1975). In order for core components of multisubunit complexes to be synthesised, de novo, in the correct compartment.

The evolutionary process of transfer of genes from organelle to nucleus is still incomplete. E.g. Herrmann and Westhoff, 2001: The partite plant genome is not in a phylogenetic equilibrium. All available data suggest that the ultimate aim of genome restructuring in the plant cell, as in the eukaryotic cell in general, is the elimination of genome compartmentation while retaining physiological compartmentation.

The frozen accident. The evolutionary process of gene transfer was underway when something happened that stopped it. E.g. von Heijne, 1986.

It’s all a question of hydrophobicity. The five-helix rule. (Anon)

Some proteins (with co-factors) cannot be imported. (Anon)

Redox control of gene expression (Allen 1993 et seq.) Vectorial electron and proton transfer exerts regulatory control over expression of genes encoding proteins directly involved in, or affecting, redox poise. This regulatory coupling requires co-location of such genes with their gene products; is indispensable; and operated continuously throughout the transition from prokaryote to eukaryotic organelle. Organelles “make their own decisions” on the basis of environmental changes affecting redox state.

Why Do Mitochondria and Chloroplasts Have Their Own Genetic Systems?

Proposed solution (hypothesis)

Why Mitochondria and Chloroplasts Have Their Own Genetic Systems

Allen, J. F. (1993) J. Theor. Biol. 165, 609-631

BacteriumEndosymbiontBioenergetic organelle

Prediction

Explanation of previous knowledge

Distribution of genes for components of oxidative phosphorylation between mitochondria and the cell nucleus

I II III IV ATPase

Matrix

Inter-membranespace

Prediction

Explanation of previous knowledge

Distribution of genes for components of photosynthetic phosphorylation between chloroplasts and the cell nucleus

cpDNA-encoded in all sequenced genomes of photosynthetic plastids

cpDNA-encoded in at least one sequenced plastid genome

Cytochrome b6/f Photosystem IPhotosystem II

A

B

Race, H. L., Herrmann, R. G. and Martin, W. (1999) Trends Genet. 15, 364-370

Prediction

Experimental results

Redox control of mitochondrial and chloroplast gene expression

D + ascorbateD + dithiothreitol

D + dithionite

D, anaerobicL + DCMU

L + DBMIBD + duroquinol

D + ferricyanide

Dark (D)

Light (L)

35S-methione labelling of newly synthesised proteins in pea leaf thylakoids

+ ferricyanide+ ascorbate

+ dithiothreitol+ dithionite

+ duroquinol+ rotenone, malonate.,dicumarol

+ cyanide, SHAM

pyruvate, malatecontrol

35S-methione labelling of newly synthesised proteins in pea leaf mitochondria

Allen, C. A. et al

Redox Report 1, 119-123

Allen, J. F. (1992) BBA 1098, 275-225 Pfannschmidt, T. et al. (1999) Nature 397, 625-628Pfannschmidt, T. et al. (1999) IUBMB Life 48, 271-276

The mitochondrial theory of ageing

Figure from:

ALLEN, J F (1996) J. Theor. Biol. 180, 135-140

Problem

The Mitochondrial Theory of Ageing predicts that offspring should inherit their mother’s acquired state of accumulated damage, but they evidently do not.

Babies are not born at the age of their mothers.

How can this be?

Proposed solution (hypothesis)

Separate sexes allows specialisation of mitochondria either as genetic templates

(female germ line) or as energy-transducing organelles performing

oxidative phosphorylation (male germ line)

ALLEN, J F (1996) J. Theor. Biol. 180, 135-140

Predictions

Explanations of previous knowledge

Mitochondria are maternally inherited

Females have a time-limited reproductive activity - oocyte mitochondria become useless as genetic templates after a certain threshold of oxidative damage is reached

Predictions (1996) now “previous knowledge” (since 1998).

Somatic, reproductive cloning should produce inherited ageing of offspring. Dolly: 7 + 4 = 11

Experimental predictions

Many….

Postscript

In silico veritas

The bucket or the searchlight?

• Which is the better metaphor for scientific enquiry - the bucket or the searchlight?

The bucket

The bucket or the searchlight?

• Even the oceans of data from DNA-microarrays, genomics (and heter-omics) cannot be converted into knowledge or understanding by being scooped up, at random, as if in bucketfuls.

• Knowledge is more than information, and cannot be deduced from it.

The searchlight Allen, J. F. (2001) EMBO Reports 2, 542-544

The bucket or the searchlight?

• Every observation presupposes an object of attention. We select what we examine with care.

• Our intention, in selecting what to look for, is to compare the results of experiments with the predictions of our hypotheses, to see if the results and predictions agree.

• So we look, purposefully, to see if our experimental data resembles our expectations. This is where computers can help us.

References– 1. Allen, J.F. (2001) Bioinformatics and discovery: induction beckons

again. BioEssays 23, 104-107– 2. Allen, J.F. (2001) In silico veritas. Data mining and automated

discovery- the truth is in there. EMBO Reports 2, 542-544 http://plantcell.lu.se/john/pdf/124.pdf

– 3. Wilkins, A. S. (2001) Why the philosophy of science actually does matter. BioEssays 23, 1-2

– http://plantcell.lu.se/john/publications.html

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– And THANK YOU FOR LISTENING!