Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans

Jayapal, Karthik P.; Lian, Wei-Ling; Glod, Frank; Sherman, David H.; Hu, Wei‐Shou

doi:10.1186/1471-2164-8-229

Cited by 47 publications

(73 citation statements)

References 60 publications

(65 reference statements)

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“…Interestingly, AICESco5349 flanks the whiE cluster (Bentley et al, 2002) encoding the enzymes to synthesise the grey polyketide spore pigment (Davis and Chater, 1990) and AICESco3250 flanks the calcium-dependent antibiotic (CDA) biosynthetic gene cluster. The two AICEs are absent on the highly syntenic core region of the S. lividans genome (Jayapal et al, 2007) and the S. ambofaciens genome lacks the CDA cluster and also the complete region containing the whiE cluster and AICESco5349 (Choulet et al, 2006). Possibly, these AICEs are associated with the acquisition of these secondary metabolite clusters in S. coelicolor.…”

Section: Discussionmentioning

confidence: 99%

Actinomycete integrative and conjugative pMEA-like elements of Amycolatopsis and Saccharopolyspora decoded

Poele

Samborskyy

Oliynyk

et al. 2008

Plasmid

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Section: Discussionmentioning

confidence: 99%

Actinomycete integrative and conjugative pMEA-like elements of Amycolatopsis and Saccharopolyspora decoded

Poele

Samborskyy

Oliynyk

et al. 2008

Plasmid

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“…These observations demonstrate that the regulatory circuits controlling the morphological differentiation process are somehow different in these two closely related species. Despite the overexpression of SCO3201, S. lividans sporulates, indicating either that some of the SCO3201 operator sites are missing in front of key genes involved in the positive regulation Indeed, it was demonstrated that some genomic islands larger than 25 kb and comprising more than 600 genes were present in the S. coelicolor genome but absent in the S. lividans genome (30). The SCO3201 regulator was shown to negatively autoregulate its own synthesis, and its operator site in its own promoter region was identified as the 15-bp palindromic sequence (TG GCAGATTCTGCCA) that is a typical binding site for homodimer transcriptional regulators of the TetR family (51).…”

Section: Discussionmentioning

confidence: 99%

Repression of Antibiotic Production and Sporulation inStreptomyces coelicolorby Overexpression of a TetR Family Transcriptional Regulator

Seghezzi

Esnault

et al. 2010

Appl Environ Microbiol

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The development of the Gram-positive genus Streptomyces is characterized by a complex morphological differentiation process thought to be triggered by conditions of nutritional limitation that often correlate with high cell density (41). This process includes the arising of an aerial mycelium from the vegetative mycelium and then the differentiation of the tips of the aerial hyphae into spores (10, 15). This process is coupled to a metabolic differentiation that correlates with the production of a wide range of pharmaceutically important secondary metabolites, including antibacterial, anticancer, and immunosuppressive drugs (8, 10). The genes responsible for the biosynthesis of these secondary metabolites are clustered in the genome and coordinately regulated by pathway-specific transcriptional regulators (1,4,18,19,62,70). The expression of these specific regulators linked to the biosynthetic pathways is directly or indirectly controlled either by positive pleiotropic regulators, such as AfsR2 (69), AfsS (29), AtrA (65), PtpA (67), PkaD (68), and the two-component systems AfsK/AfsR (66) and EcrA1/EcrA2 (39), by negative regulators, including the two-component systems AbsA1/AbsA2 (44), PhoR/PhoP (55), and CutR/CutS (9), or by enzymatic systems, such as Ppk (16). The pleiotropic regulators, thought to sense a variety of extracellular or intracellular signals related to nutriment availability, cell crowding, or energy shortage, are necessary to trigger the necessary metabolic adjustments to adapt to these conditions (27, 43), whereas the ppk gene is thought to act as an ATP-regenerating enzyme (54).Streptomyces coelicolor A3 (2) is usually used as the reference strain to study morphological and metabolic differentiation in relation with antibiotic biosynthesis (10, 15). S. coelicolor has long been known to produce four major antibiotics, actinorhodin (ACT) (40), undecylprodigiosin (RED) (13), methylenomycin (MMY) (36), and calcium-dependent antibiotic (CDA) (21), and recently, two novel ones were characterized, CPK, a putative type I polyketide (17, 50), and albaflavenone, a sesquiterpene antibiotic (72). ACT is a secondary metabolite of the polyketide family that is strongly produced by S. coelicolor but only weakly produced by its close relative, Streptomyces lividans. However, S. lividans has the genetic capability to produce this compound since the weak production of ACT could be stimulated by various genetic manipulations that include the overexpression of the pathway-specific activator gene actII-ORF4 (7), the afsR and afsR2 (now afsS) genes (35), the rep gene (42), and the phosphotyrosine protein phosphataseencoding gene ptpA (67). The inactivation of other genes, such as ppk (11), or mutations in the rpoB gene (25) or in the ribosomal protein S12 (23) are also leading to an enhancement of ACT production, indicating that ACT production was subjected to complex positive and negative controls. Furthermore, the extracellular addition of the signal molecule S-adenosylmethionine (34) or of ATP (38) or the replac...

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“…Identification of gene divergence or absence has already been thoroughly investigated in many closely related organisms (21,24,29,41,43). Often, loss or alteration of genetic content is affected by the activity of IS elements (7,28).…”

Section: Discussionmentioning

confidence: 99%

“…paratuberculosis (49) and Tropheryma whipplei strains (27). In addition, the absence of five Streptomyces coelicolor genomic islands were reported in Streptomyces lividans (24), and differences in gene content were detected in other species, Salmonella enterica (38) and Xylella fastidiosa (26). In this work we compared the genomes of nine strains of L. helveticus which were isolated from the dairy environment.…”

mentioning

confidence: 99%

Crucial Role for Insertion Sequence Elements in Lactobacillus helveticus Evolution as Revealed by Interstrain Genomic Comparison

Kaleta

O’Callaghan

Fitzgerald

et al. 2010

Appl Environ Microbiol

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Lactobacillus helveticus is a versatile dairy bacterium found to possess heterogeneous genotypes depending on the ecosystem from which it was isolated. The recently published genome sequence showed the remarkable flexibility of its structure, demonstrated by a substantial level of insertion sequence (IS) element expansion in association with massive gene decay. To assess this diversity and examine the level of genome plasticity within the L. helveticus species, an array-based comparative genome hybridization (aCGH) experiment was designed in which 10 strains were analyzed. The aCGH experiment revealed 16 clusters of open reading frames (ORFs) flanked by IS elements. Four of these ORFs are associated with restriction/modification which may have played a role in accelerated evolution of strains in a commercially intensive ecosystem undoubtedly challenged through successive phage attack. Furthermore, analysis of the IS-flanked clusters demonstrated that the most frequently encountered ISs were also those most abundant in the genome (IS1201, ISL2, ISLhe1, ISLhe2, ISLhe65, and ISLhe63). These findings contribute to the overall viewpoint of the versatile character of IS elements and the role they may play in bacterial genome plasticity.Lactobacillus helveticus is a gram-positive, homofermentative lactic acid bacterium which is widely used in the manufacture of cheeses, such as Swiss cheese and some Cheddar-type cheeses (22,25). It is also commonly used in the production of different types of Italian cheeses, such as Parmigiano Reggiano (18) and Grana Padano, where it contributes to the formation of specific flavor compounds (42).Phylogenetic analysis of ribosomal protein sequences derived from lactobacilli and streptococci classified L. helveticus in the same group along with both gastrointestinal (GI) tract and dairy-specific species (14). Comparative analysis of the 16S rRNA of L. helveticus DPC4571 revealed 98.4% identity with Lactobacillus acidophilus NCFM and indicated that this probiotic strain was closely related to strain DPC4571, despite the different environments these two lactobacilli inhabit (4). The results of genomic analysis of L. helveticus suggested that two major events have occurred in the diversification process of L. helveticus from a common ancestor with L. acidophilus, selective gene loss and acquisition of a large number of insertion sequence (IS) elements (4). IS elements are DNA sequences capable of independent transposition within and between bacterial genomes (31). Their capacity for independent mobility demonstrates the parasitic nature of these elements (11); however, they can also be regarded as having a positive influence, as they assist in promoting genetic variation (1). Thus, even though the primal character of these elements remains unclear in that they may be considered simply as selfish DNA elements, their impact on the architecture of microbial genomes is undeniable. It has already been demonstrated that IS-related mutations occur in Escherichia coli (44), Lactococcus lactis (10)...

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Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans

Cited by 47 publications

References 60 publications

Actinomycete integrative and conjugative pMEA-like elements of Amycolatopsis and Saccharopolyspora decoded

Actinomycete integrative and conjugative pMEA-like elements of Amycolatopsis and Saccharopolyspora decoded

Repression of Antibiotic Production and Sporulation inStreptomyces coelicolorby Overexpression of a TetR Family Transcriptional Regulator

Crucial Role for Insertion Sequence Elements in Lactobacillus helveticus Evolution as Revealed by Interstrain Genomic Comparison

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