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 beta-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.

FIG. 1.

Circular representation of the M. luteus chromosome. Genome coordinates are given in Mbp. From outside to inside, the various circles represent genes on the forward strand, genes on the reverse strand, RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, and GC skew. Genes are color coded according to their COG category. The color code of function category for top COG hit is shown in Table S4 in the supplemental material.

FIG. 2.

Percentage of genes assigned to different COG categories in M. luteus and related organisms.

FIG. 3.

Synteny between actinobacterial genomes. For each genome the first gene is dnaA, except in the case of the linear S. coelicolor genome, in which dnaA is located centrally. Each dot represents a reciprocal best match (BLASTp) between proteins in the genomes being compared. Dots are positioned according to their genome locations. See Materials and Methods for further details. Abbreviations: Mlu, Micrococcus luteus; Krh, Kocuria rhizophila (123); Art, Arthrobacter sp. strain FB24; Cmm, Clavibacter michiganensis subsp. michiganensis (32); Mtb, Mycobacterium tuberculosis (22); Sco, Streptomyces coelicolor (11); Rsa, Renibacterium salmoninarum (137).

FIG. 4.

Proposed integrated elements (IEs) in M. luteus Fleming. Block arrows containing numbers represent ORFs and their %GC values. The proposed function of the gene products is shown where predictions from database searches are informative. All four of the proposed IEs are within regions of lower than average %GC for M. luteus, and three of the elements (IEMlut1, IEMlut2, and IEMlut4) interrupt regions with good synteny with Arthrobacter. The ORFs are colored as follows: brown indicates synteny of gene order with Arthrobacter; gray indicates that the gene product might be involved in plasmid replication or transfer; green is a transposase or fragment thereof; red is used to highlight the putative metal resistance genes. A and B. IEMlut1 (approximate coordinates 11840 to 72798) and IEMlut2 (approximate coordinates 672329 to 680904) may have been integrated via the serine integrases, Mlut_00100 and Mlut_06210, respectively. The putative DnaK, GrpE, and DnaJ and the ClpB-like chaperone genes (Mlut_00560 to Mlut00580, Mlut_00600) have been included in IEMlut1 since they appear to have been acquired horizontally. Their closest relatives are not the paralogous genes on the M. luteus chromosome (Mlut_11810, Mlut_11800, Mlut_11790, and Mlut_18660) but genes from other actinomycetes such as Streptomyces sp., Catenulispora, and Gordonia. On the other hand, the closest relatives of Mlut_11790, Mlut_11800, and Mlut_18660 are from the phylogenetically close Arthrobacter and Kocuria. IEMlut2 appears to have inserted into a putative oxidoreductase to yield two gene fragments, Mlut_06130 and Mlut_06220 (yellow). (C and D) IEMlut3 (approximate coordinates 695571 to 717542) and IEMlut4 (approximate coordinates 2223379 to 2238868) may have integrated via the action of the conserved triplet of genes that includes two tyrosine recombinases (the closest homologues are either purple [Mlut_06600 and Mlut_20690] or light blue [Mlut_06590 and Mlut_20700]) and a conserved hypothetical (CH; colored blue-green) (Mlut_06610 and Mlut_20680).

FIG. 5.

Conservation of division/cell wall (DCW) clusters. The DCW clusters of several bacteria are schematically represented. Coding sequences are not drawn to scale, in order to facilitate alignment. The triangles denote the positions of single gene insertions unless numerals are present that indicate the insertion of multiple genes. Where orthologues are absent from the cluster but retained at a locus nearby, they are placed to one side. The key to the gene symbols placed above each cluster are as follows: Z, mraZ; W, mraW; L, ftsL; I, ftsI; I′, spoVD; E, murE; Y, mraY; D, murD; Fw, ftsW; G, murG; C, murC; B, murB, Dd, ddlB; Q, ftsQ; A, ftsA; Fz, ftsZ.

FIG. 6.

Organization of the ole (olefin synthesis) genes in M. luteus and other bacteria.