| Abstract: | Micrococcus luteus (NCTC2665, “Fleming strain”) has one of the smallest genomes of free-living actinobacteria sequenced to date, comprising a single circular chromosome of 2,501,097 bp (G+C content, 73%) predicted to encode 2,403 proteins. The genome shows extensive synteny with that of the closely related organism, Kocuria rhizophila, from which it was taxonomically separated relatively recently. Despite its small size, the genome harbors 73 insertion sequence (IS) elements, almost all of which are closely related to elements found in other actinobacteria. An IS element is inserted into the rrs gene of one of only two rrn operons found in M. luteus. The genome encodes only four sigma factors and 14 response regulators, a finding indicative of adaptation to a rather strict ecological niche (mammalian skin). The high sensitivity of M. luteus to β-lactam antibiotics may result from the presence of a reduced set of penicillin-binding proteins and the absence of a wblC gene, which plays an important role in the antibiotic resistance in other actinobacteria. Consistent with the restricted range of compounds it can use as a sole source of carbon for energy and growth, M. luteus has a minimal complement of genes concerned with carbohydrate transport and metabolism and its inability to utilize glucose as a sole carbon source may be due to the apparent absence of a gene encoding glucokinase. Uniquely among characterized bacteria, M. luteus appears to be able to metabolize glycogen only via trehalose and to make trehalose only via glycogen. It has very few genes associated with secondary metabolism. In contrast to most other actinobacteria, M. luteus encodes only one resuscitation-promoting factor (Rpf) required for emergence from dormancy, and its complement of other dormancy-related proteins is also much reduced. M. luteus is capable of long-chain alkene biosynthesis, which is of interest for advanced biofuel production; a three-gene cluster essential for this metabolism has been identified in the genome.Micrococcus luteus, the type species of the genus Micrococcus (family Micrococcaceae, order Actinomycetales) (117), is an obligate aerobe. Three biovars have been distinguished (138). Its simple, coccoid morphology delayed the recognition of its relationship to actinomycetes, which are typically morphologically more complex. In the currently accepted phylogenetic tree of the actinobacteria, Micrococcus clusters with Arthrobacter and Renibacterium. Some other coccoid actinobacteria originally also called Micrococcus, but reclassified into four new genera (Kocuria, Nesterenkonia, Kytococcus, and Dermacoccus), are more distant relatives (121). The genus Micrococcus now includes only five species: M. luteus, M. lylae, M. antarcticus, M. endophyticus, and M. flavus (20, 69, 70, 121).We report here the genome sequence of Micrococcus luteus NCTC2665 (DSM 20030T), a strain of historical interest, since Fleming used it to demonstrate bacteriolytic activity (due to lysozyme) in a variety of body tissues and secretions (29, 30), leading to its designation as Micrococcus lysodeikticus until its taxonomic status was clarified in 1972 (59). M. luteus has been used in a number of scientific contexts. The ease with which its cell wall could be removed made it a favored source of bacterial cell membranes and protoplasts for investigations in bioenergetics (28, 34, 89, 93). Because of the exceptionally high GC content of its DNA, M. luteus was used to investigate the relationship between codon usage and tRNA representation in bacterial genomes (51, 52, 61). Although it does not form endospores, M. luteus can enter a profoundly dormant state, which could explain why it may routinely be isolated from amber (39). Dormancy has been convincingly demonstrated under laboratory conditions (53-55, 83), and a secreted protein (Rpf) with muralytic activity is involved in the process of resuscitation (81, 82, 84, 85, 87, 125, 133).Micrococci are also of biotechnological interest. In addition to the extensive exploitation of these and related organisms by the pharmaceutical industry for testing and assaying compounds for antibacterial activity, micrococci can synthesize long-chain alkenes (1, 2, 127). They are also potentially useful for ore dressing and bioremediation applications, since they are able to concentrate heavy metals from low-grade ores (26, 66, 67, 116).Given its intrinsic historical and biological importance, and its biotechnological potential, it is perhaps surprising that the genome sequence of M. luteus was not determined previously (130). We consider here the strikingly small genome sequence in these contexts and also in relation to the morphological simplicity of M. luteus compared to many of its actinobacterial relatives, which include important pathogens as well as developmentally complex, antibiotic-producing bacteria with some of the largest bacterial genomes. |
