Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium

Michael Young, Vladislav Artsatbanov, Harry R. Beller, Govind Chandra, Keith F. Chater, Lynn G. Dover, Ee-Been Goh, Tamar Kahan, Arseny S. Kaprelyants, Nikos Kyrpides, Alla Lapidus, Stephen R. Lowry, Athanasios Lykidis, Jacques Mahillon, Victor Markowitz, Konstantinos Mavromatis, Galina V. Mukamolova, Aharon Oren, J. Stefan Rokem, Margaret C. Smith & 2 others Danielle I. Young, Charles L. Greenblatt

Research output: Contribution to journalArticle

36 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)841-860
Number of pages20
JournalJournal of Bacteriology
Volume192
Issue number3
DOIs
Publication statusPublished - Feb 2010

Keywords

  • resuscitation-promoting factors
  • penicillin-binding proteins
  • streptomyces-coelicolor A3(2)
  • stationary-phase cultures
  • mycobacterium-tuberculosis
  • corynebacterium-glutamicum
  • escherichia-coli
  • cell-division
  • teichuronic acid
  • sarcina-lutea

Cite this

Young, M., Artsatbanov, V., Beller, H. R., Chandra, G., Chater, K. F., Dover, L. G., ... Greenblatt, C. L. (2010). Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium. Journal of Bacteriology, 192(3), 841-860. https://doi.org/10.1128/JB.01254-09

Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium. / Young, Michael; Artsatbanov, Vladislav; Beller, Harry R.; Chandra, Govind; Chater, Keith F.; Dover, Lynn G.; Goh, Ee-Been; Kahan, Tamar; Kaprelyants, Arseny S.; Kyrpides, Nikos; Lapidus, Alla; Lowry, Stephen R.; Lykidis, Athanasios; Mahillon, Jacques; Markowitz, Victor; Mavromatis, Konstantinos; Mukamolova, Galina V.; Oren, Aharon; Rokem, J. Stefan; Smith, Margaret C.; Young, Danielle I.; Greenblatt, Charles L.

In: Journal of Bacteriology, Vol. 192, No. 3, 02.2010, p. 841-860.

Research output: Contribution to journalArticle

Young, M, Artsatbanov, V, Beller, HR, Chandra, G, Chater, KF, Dover, LG, Goh, E-B, Kahan, T, Kaprelyants, AS, Kyrpides, N, Lapidus, A, Lowry, SR, Lykidis, A, Mahillon, J, Markowitz, V, Mavromatis, K, Mukamolova, GV, Oren, A, Rokem, JS, Smith, MC, Young, DI & Greenblatt, CL 2010, 'Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium', Journal of Bacteriology, vol. 192, no. 3, pp. 841-860. https://doi.org/10.1128/JB.01254-09
Young, Michael ; Artsatbanov, Vladislav ; Beller, Harry R. ; Chandra, Govind ; Chater, Keith F. ; Dover, Lynn G. ; Goh, Ee-Been ; Kahan, Tamar ; Kaprelyants, Arseny S. ; Kyrpides, Nikos ; Lapidus, Alla ; Lowry, Stephen R. ; Lykidis, Athanasios ; Mahillon, Jacques ; Markowitz, Victor ; Mavromatis, Konstantinos ; Mukamolova, Galina V. ; Oren, Aharon ; Rokem, J. Stefan ; Smith, Margaret C. ; Young, Danielle I. ; Greenblatt, Charles L. / Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium. In: Journal of Bacteriology. 2010 ; Vol. 192, No. 3. pp. 841-860.
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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.",
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T1 - Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium

AU - Young, Michael

AU - Artsatbanov, Vladislav

AU - Beller, Harry R.

AU - Chandra, Govind

AU - Chater, Keith F.

AU - Dover, Lynn G.

AU - Goh, Ee-Been

AU - Kahan, Tamar

AU - Kaprelyants, Arseny S.

AU - Kyrpides, Nikos

AU - Lapidus, Alla

AU - Lowry, Stephen R.

AU - Lykidis, Athanasios

AU - Mahillon, Jacques

AU - Markowitz, Victor

AU - Mavromatis, Konstantinos

AU - Mukamolova, Galina V.

AU - Oren, Aharon

AU - Rokem, J. Stefan

AU - Smith, Margaret C.

AU - Young, Danielle I.

AU - Greenblatt, Charles L.

PY - 2010/2

Y1 - 2010/2

N2 - 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.

AB - 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.

KW - resuscitation-promoting factors

KW - penicillin-binding proteins

KW - streptomyces-coelicolor A3(2)

KW - stationary-phase cultures

KW - mycobacterium-tuberculosis

KW - corynebacterium-glutamicum

KW - escherichia-coli

KW - cell-division

KW - teichuronic acid

KW - sarcina-lutea

U2 - 10.1128/JB.01254-09

DO - 10.1128/JB.01254-09

M3 - Article

VL - 192

SP - 841

EP - 860

JO - Journal of Bacteriology

JF - Journal of Bacteriology

SN - 0021-9193

IS - 3

ER -