Organelle Genomics

Published in Probe Volume 6 (Final): July 1996

Tim Littlejohn
Departement de Biochimie
Universite de Montreal
C.P. 6128, succursale Centre-ville
Montreal (Quebec), CANADA

Symbioses

Mutually beneficial symbiotic relationships are common in biology, in both nature and the scientific process. Symbiotic events have characterized the evolution of eukaryotes (Gray 1992) as cells joined forces to create new, more successful forms. Indeed, the present day plant genome is a composite of at least two such (endosymbiotic) events, resulting in three distinct genomes within the cell (plastid, mitochondrion and nucleus; fig. 1).

The origins and information content of organelle genomes is being dissected by an alliance of Canadian research groups, which has brought together individuals with a diversity of expertise. Two separate endeavors, an organelle genome sequencing program and an organelle database project, are cooperating to create a focus of organelle genomics (fig. 1).

OGMP-an organelle genome program

The OGMP (Organelle Genome Megasequencing Program) is a collaborative effort of Canadian research groups with expertise in genomics, evolution, mathematics, and informatics, united under the umbrella of the CIAR (Canadan Institute for Advanced Research) Program in Evolutionary Biology (table 1). The multidisciplinary approach of the OGMP is an essential component of any genomics program, where the generation and management of large quantities of data requires broad and deep skills across the fields of biology and computer science.

The goal of the OGMP since its inception in 1992 has been to generate a phylogenetically diverse collection of organelle genome sequences to delve into the mode and tempo of organelle genome evolution. The OGMP is generating a quantity of data that should permit assessment of how (and the number of times) plastids and mitochondria arose, how their genomes have changed, and what accounts for the different evolutionary patterns they display. One focus of the OGMP has been to resolve the phylogenetic relationships between the major protist phyla such as ciliates, rhodophytes, cryptophytes, stramenopiles, and rhizopods. Another emphasis has been to investigate the base of the evolutionary bifurcation between the green lineages of the charophytes/embryophytes and the chlorophytes. These questions, which have proven to be intractable with single gene sequences, have been resolved using the large data sets of complete mitochondrial sequences (over 475 kb of new organelle sequences so far--table 2; OGMP, in preparation).

The OGMP is structured into two components, the Team and the Sequencing Unit that work together for mutual benefit. (fig. 1). The Team, composed of the seven collaborating research groups, decides on the overall directions of the program and provides the raw material (purified organellar DNA) to the Unit. The Unit then clones and sequences the supplied DNA, manages the production of the complete genome sequence, and performs analysis of gene content and organization. Completed genome sequences are further analyzed in collaboration with the Team, which continues analysis (for examples, phylogenetics) and uses this information to guide the selection of additional key genomes to be sequenced and the planning of spin-off projects (for example, the modes of mitochondrial gene expression).

The Sequencing Unit is further divided into two components: the Molecular Biology Division (MBD) and the Informatics Division (ID). The Molecular Biology Division is charged with performing all the molecular biology within the Unit as well as with the overall project management and analysis. The Informatics Divisions mission is to support the Molecular Biology Division for all their computing requirements (software, hardware, databases, networks) and to conduct bioinformatics research. The large quantity of data generated by the OGMP necessitates that nearly 45 percent of its resources be channeled into informatics, which has proven to be pivotal for data management, analysis, and decision support (Burger et al., in preparation).

GOBASE-an integrated database for organelle genomics

As a new initiative, the goal of the GOBASE project is to construct an organelle genome database, integrating all the information generated by the OGMP and other organelle genome research groups. The GOBASE database will:

serve as an integrated, centralized repository for all organelle information
include data from nucleic acid and protein sequences, polymorphisms, and genetic and physical maps to biochemical and physiological data
model organelle RNA secondary structures
facilitate organelle data submission from the community
develop novel approaches to database integration and genomic data analysis

GOBASE will provide a framework for the access to, and analysis of, organelle data, including: comparative genomics, molecular biology, evolutionary biology, population genetics, and biogenesis. The GOBASE project invites comments and suggestions for its development from the community (see table 1 for contact information).

Future and further information

Genomics is unquestionably one of the most exciting movements in biology today, and organelle genomes continue to provide the most exhaustive set of completely sequenced cellular genomes (with over 50 complete sequences presently available in GenBank and growing by more than 3 genomes per year by the OGMP effort alone; Littlejohn 1994). The Canadian Organelle Genomics group will continue to rely on multidisciplinary, symbiotic relationships for its progress, linking expertise in organismal biology, molecular biology, evolution, and informatics. A dataset of this size permits comparative studies that reveal much about genome structure, function and evolution.

Further information on the projects can be obtained at the following World Wide Web sites: OGMP:

http://megasun.bch.umontreal.ca/ogmp/welcome.html

GOBASE:

http://gobase.bcm.umontreal.ca/ or by e-mail (table 1).

Acknowledgments

This work was supported by the Canadian Institute for Advanced Research, the Canadian Genome Analysis and Technology Program Grants GO-12323 & GO-12984, The Medical Research Council, Canada, Program Grant SP-34, and an Academic Equipment Grant from Sun Microsystems. Thanks to Jenny Saleeba, Gertraud Burger, and B. Franz Lang for comments on the manuscript.

References

Burger, G., I. Plante, K.M. Lonergan and others. 1995. "The mitochondrial DNA of the amoeboid protozoon, Acanthamoeba castellanii. Complete sequence, gene content and genome organization." Journal of Molecular Biology 245:522-537.

Gray, M.W. 1992. In K.W. Jeon and D.R. Wolsstenhome, eds, "The endosymbiont hypothesis revisited." International Review of Cytology, Special Volume of Mitochondrial Genomes 141:233-357.

Littlejohn, T.G. 1994. "Organelle genome data--whole genome sequences." URL: gopher://megasun.bch.umontreal.ca:70/11/Organelles/Genomes

Wolff, G., B.F. Lang . 1993a. "The mitochondrial genome of Prototheca wickerhamii." In S.J. O'Brien, ed., Genetic Maps, Cold Spring Harbor Laboratory Press, 2:172

Wolff, G., G. Burger, B.F. Lang and others. 1993b. "Mitochondrial genes in the colorless alga Prototheca wickerhamii resemble plant genes in their exons but fungal genes in their introns." Nucleic Acids Research 21:719-726.

Wolff, G., I. Plante, B.F. Lang and others. 1994. "Complete sequence of the mitochondrial DNA of the chlorophyte alga Prototheca wickerhamii. Gene content and genome organization." Journal of Molecular Biology 237:74-86.