Genome Sequence of the Fleming Strain of Micrococcus luteus , a Simple Free-Living Actinobacterium

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 ␤-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 20030 T ), a strain of historical interest, since Fleming used it to demonstrate bacteriolytic activity (due to lysozyme) in a variety of body tissues and secretions (29,3...

Beyond Asexual Development: Modifications in the Gene Expression Profile Caused by the Absence of the Aspergillus nidulans Transcription Factor FlbB

“…The metabolite linked to the activity of the dba cluster, DHMBA, has shown biological activity against the bacterium M. luteus , an obligate aerobe found in soil, dust, water, and air and in a number of body tissues and secretions (Young et al 2010). To verify the levels of activation and relevance of the dba cluster in the successful competition of A. nidulans with bacterial species, we cocultured DflbB strains (in which expression of dba cluster genes was induced as shown earlier) with M. luteus under experimental conditions suited to accurate quantitative analysis (bacteria/conidia = 25/1) ( Figure 6A; see also Materials and Methods).…”

Biosynthetic Pathway for γ-Cyclic Sarcinaxanthin in Micrococcus luteus : Heterologous Expression and Evidence for Diverse and Multiple Catalytic Functions of C 50 Carotenoid Cyclases

“…The genome sequence of M. luteus strain NCTC2665 (accession number NC_012803) has been deposited in the databases, and just before the submission of this paper, an accompanying publication appeared in the scientific literature (47). In silico screening of the sequence data resulted in the identification of a putative carotenoid biosynthesis gene cluster consisting of a total of nine open reading frames, or1007 to or1015.…”

A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes

“…Plotting all known cases of nuclear genetic code reassignments onto the codon table shows that most cases resulted from extending the decoding capabilities of near-cognate tRNAs. Reassignments reported for Mycoplasma capricolum, which was thought to lack a dedicated tRNA for decoding CGG although still containing six CGG codons in its genome (Oba et al 1991), and Micrococcus luteus, which was thought to lack AUA and AGA codons (Kano et al 1993), are not supported by whole-genome sequencing data (Young et al 2010;Chu et al 2011). The available data show that the Caenorhabditis elegans GGG codons are translated as glycine in vivo and not as leucine (Hamashima et al 2015).…”