The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont Sinorhizobium meliloti suggest a recent evolutionary divergence. Their similarities include metabolic, transport, and regulatory systems that promote survival in the highly competitive rhizosphere; differences are apparent in their genome structure and virulence gene complement. Availability of the A. tumefaciens sequence will facilitate investigations into the molecular basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles.

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The genome sequence of the genetically tractable, mesophilic, hydrogenotrophic methanogen Methanococcus maripaludis contains 1,722 protein-coding genes in a single circular chromosome of 1,661,137 bp. Of the protein-coding genes (open reading frames [ORFs]), 44% were assigned a function, 48% were conserved but had unknown or uncertain functions, and 7.5% (129 ORFs) were unique to M. maripaludis. Of the unique ORFs, 27 were confirmed to encode proteins by the mass spectrometric identification of unique peptides. Genes for most known functions and pathways were identified. For example, a full complement of hydrogenases and methanogenesis enzymes was identified, including eight selenocysteine-containing proteins, with each being paralogous to a cysteine-containing counterpart. At least 59 proteins were predicted to contain iron-sulfur centers, including ferredoxins, polyferredoxins, and subunits of enzymes with various redox functions. The methanogenic Archaea (methanogens) occupy a unique metabolic niche, as they produce methane, which is a useful energy source and a powerful greenhouse gas. These organisms are found in diverse anaerobic habitats, ranging from aquatic and marine sediments to sewage digesters and the rumens and large intestines of herbivores and other mammals (127). In these habitats, the degradation of organic matter results in the production of H 2 and other intermediates by fermentative organisms. By maintaining an extremely low partial pressure of H 2 , the methanogens keep fermentative pathways energetically favorable. In addition, some methanogens may occupy niches where hydrogen is produced predominately by geothermal reactions.Metabolically, methanogens are divided into those that specialize in CO 2 reduction and those that also use acetate and/or methyl compounds. The former group, the hydrogenotrophs, use H 2 as an electron donor to reduce CO 2 to methane. Many hydrogenotrophic species can substitute formate or certain low-molecular-weight alcohols and ketones for H 2 . Complete genome sequences have been published for three hydrogenotrophic methanogens, Methanocaldococcus jannaschii (13), Methanothermobacter thermautotrophicus (105), and Methanopyrus kandleri (104), all of which are thermophiles or hyperthermophiles. Of the methanogens that utilize acetate and methyl compounds, complete genome sequences have been published for two species, Methanosarcina acetivorans (26) and Methanosarcina mazei (19), both of which are mesophiles. In addition, partial sequences have been published for two psychrophiles, the hydrogenotroph Methanogenium frigidum and the methylotroph Methanolobus burtonii (97).Genome sequences of methanogens have answered many questions, but they have inspired many others. More than half of the genes in Methanocaldococcus jannaschii lack a predicted function (13), and this proportion has not declined significantly as other methanogen sequences have been determined. The proportions of genes of unknown functions, which are either homologous to other genes of unknown function...