Many endosymbiotic bacteria -- bacteria that live with the body or cells of another organism -- undergo genome reduction as they adapt to intracellular life within their hosts. Now two studies reported in the 13 Oct 2006 Science defy previous notions of how small these genomes can become. Both genomes -- the smallest sequenced to date -- derive from insect symbionts and have lost important genes functions that threaten the very existence of these microbes. Pérez-Brocal et al. ( http://www.sciencemag.org/cgi/content/short/314/5797/312 ) reported on the ~422-kilobase-pair genome of the aphid symbiont Buchnera aphidicola. This bacterium has lost most metabolic functions, including the ability to synthesize riboflavin and the essential amino acid tryptophan. The researchers suggest that these losses are being complemented, and might eventually be replaced by, a coexisting secondary symbiont. Nakabachi et al. ( http://www.sciencemag.org/cgi/content/short/314/5797/267 ) described the even smaller genome of Carsonella ruddii -- a symbiont of phloem-sap-feeding insects. Its ~160-kb chromosome encodes no more than 182 proteins and is missing numerous genes considered essential for life, including those for transport and membrane synthesis. Rather than being replaced by a secondary symbiont, the team surmises that as in the case of organelles, the lost genes may have been transferred to the host nuclear genome. As noted in an accompanying Perspective by S.G.E. Andersson ( http://www.sciencemag.org/cgi/content/short/314/5797/259 ), future studies of these and other tiny bacterial genomes will provide clues about organelle evolution and the various routes taken to minimal gene-sets in nature.

COHscientist:

These articles really point toward the complexity of evolutionary biology, but also raises one of the most intriguing microbiological questions: What is the minimal set of genes necessary for cellular life.


For those of you interested in the study of minimal genomes within endosymbiotic bacteria, here are a few good references:


Arcady R. Mushegian and Eugene V. Koonin. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. PNAS, Sep 1996; 93: 10268 - 10273.

Abstract
The recently sequenced genome of the parasitic bacterium Mycoplasma genitalium contains only 468 identified protein-coding genes that have been dubbed a minimal gene complement [Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., et al. (1995) Science 270, 397-403]. Although the M. genitalium gene complement is indeed the smallest among known cellular life forms, there is no evidence that it is the minimal self-sufficient gene set. To derive such a set, we compared the 468 predicted M. genitalium protein sequences with the 1703 protein sequences encoded by the other completely sequenced small bacterial genome, that of Haemophilus influenzae. M. genitalium and H. influenzae belong to two ancient bacterial lineages, i.e., Gram-positive and Gram-negative bacteria, respectively. Therefore, the genes that are conserved in these two bacteria are almost certainly essential for cellular function. It is this category of genes that is most likely to approximate the minimal gene set. We found that 240 M. genitalium genes have orthologs among the genes of H. influenzae. This collection of genes falls short of comprising the minimal set as some enzymes responsible for intermediate steps in essential pathways are missing. The apparent reason for this is the phenomenon that we call nonorthologous gene displacement when the same function is fulfilled by nonorthologous proteins in two organisms. We identified 22 nonorthologous displacements and supplemented the set of orthologs with the respective M. genitalium genes. After examining the resulting list of 262 genes for possible functional redundancy and for the presence of apparently parasite-specific genes, 6 genes were removed. We suggest that the remaining 256 genes are close to the minimal gene set that is necessary and sufficient to sustain the existence of a modern-type cell. Most of the proteins encoded by the genes from the minimal set have eukaryotic or archaeal homologs but seven key proteins of DNA replication do not. We speculate that the last common ancestor of the three primary kingdoms had an RNA genome. Possibilities are explored to further reduce the minimal set to model a primitive cell that might have existed at a very early stage of life evolution.

Link
http://www.pnas.org/cgi/content/abstract/93/19/10268



A. Goffeau, B. G. Barrell, H. Bussey, et al. Life with 6000 Genes
Science 25 October 1996. Vol. 274. no. 5287, pp. 546 - 567
DOI: 10.1126/science.274.5287.546

Abstract
The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.

Link
http://www.sciencemag.org/cgi/content/abstract/274/5287/546


Howard Ochman, Nancy A. Moran. Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis
Science 11 May 2001, Vol. 292. no. 5519, pp. 1096 - 1099
DOI: 10.1126/science.1058543

Abstract
Traditionally, evolutionary biologists have viewed mutations within individual genes as the major source of phenotypic variation leading to adaptation through natural selection, and ultimately generating diversity among species. Although such processes must contribute to the initial development of gene functions and their subsequent fine-tuning, changes in genome repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens and symbionts. Furthermore, pathogens and symbionts depend on similar mechanisms for interacting with hosts and show parallel trends in genome evolution.

Link
http://www.sciencemag.org/cgi/content/abstract/292/5519/1096



Rosario Gil, Beatriz Sabater-Muoz, Amparo Latorre, Francisco J. Silva, and Andrés Moya. Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life. PNAS, Mar 2002; doi:10.1073/pnas.062067299

Abstract
Buchnera is a mutualistic intracellular symbiont of aphids. Their association began about 200 million years ago, with host and symbiont lineages evolving in parallel since that time. During this coevolutionary process, Buchnera has experienced a dramatic decrease of genome size, retaining only essential genes for its specialized lifestyle. Previous studies reported that genome size in Buchnera spp. is very uniform, suggesting that genome shrinkage occurred early in evolution, and that modern lineages retain the genome size of a common ancestor. Our physical mapping of Buchnera genomes obtained from five aphid lineages shows that the genome size is not conserved among them, but has been reduced down to 450 kb in some species. Here we show evidence of six species with a genome size smaller than Mycoplasma genitalium, the smallest bacterial genome reported thus far (580 kb). Our findings strongly suggest that the Buchnera genome is still experiencing a reductive process toward a minimum set of genes necessary for its symbiotic lifestyle.

Link
http://www.pnas.org/cgi/content/full/062067299v1