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Link to original content: https://pubmed.ncbi.nlm.nih.gov/18375553
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Comparative Study
. 2008 Jun;190(11):4050-60.
doi: 10.1128/JB.00204-08. Epub 2008 Mar 28.

Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350

Yasuo Ohnishi  1 , Jun Ishikawa, Hirofumi Hara, Hirokazu Suzuki, Miwa Ikenoya, Haruo Ikeda, Atsushi Yamashita, Masahira Hattori, Sueharu Horinouchi
Affiliations
Comparative Study

Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350

Yasuo Ohnishi et al. J Bacteriol. 2008 Jun.

Abstract

We determined the complete genome sequence of Streptomyces griseus IFO 13350, a soil bacterium producing an antituberculosis agent, streptomycin, which is the first aminoglycoside antibiotic, discovered more than 60 years ago. The linear chromosome consists of 8,545,929 base pairs (bp), with an average G+C content of 72.2%, predicting 7,138 open reading frames, six rRNA operons (16S-23S-5S), and 66 tRNA genes. It contains extremely long terminal inverted repeats (TIRs) of 132,910 bp each. The telomere's nucleotide sequence and secondary structure, consisting of several palindromes with a loop sequence of 5'-GGA-3', are different from those of typical telomeres conserved among other Streptomyces species. In accordance with the difference, the chromosome has pseudogenes for a conserved terminal protein (Tpg) and a telomere-associated protein (Tap), and a novel pair of Tpg and Tap proteins is instead encoded by the TIRs. Comparisons with the genomes of two related species, Streptomyces coelicolor A3(2) and Streptomyces avermitilis, clarified not only the characteristics of the S. griseus genome but also the existence of 24 Streptomyces-specific proteins. The S. griseus genome contains 34 gene clusters or genes for the biosynthesis of known or unknown secondary metabolites. Transcriptome analysis using a DNA microarray showed that at least four of these clusters, in addition to the streptomycin biosynthesis gene cluster, were activated directly or indirectly by AdpA, which is a central transcriptional activator for secondary metabolism and morphogenesis in the A-factor (a gamma-butyrolactone signaling molecule) regulatory cascade in S. griseus.

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Figures

FIG. 1.
FIG. 1.
Schematic representation of the S. griseus chromosome. (i) DraI physical map. Fragments observed after pulsed-field gel electrophoresis are indicated above the bar. The largest fragment, X, was not detected by Southern blotting using linkage clones as probes. The yellow color indicates the “core region.” (ii) Distribution of ORFs according to direction of transcription (positive strand, upper line; negative strand, lower line). (iii) Distribution of genes that were affected by adpA disruption shown by DNA microarray analysis (P < 0.05, n = 4). Red, >2-fold upregulated in the wt strain in comparison with the ΔadpA mutant; blue, >2-fold downregulated in comparison with the ΔadpA mutant. (iv) Distribution of secondary metabolite gene clusters. Red, streptomycin (str, sts); orange, grixazone (gri); green, PKS and/or NRPS; black, other. Six secondary metabolite gene clusters, the transcription of which is affected by adpA disruption, are indicated as numerals above the line. 1, SGR443 to SGR455 (NRPS); 2, SGR574 to SGR593 (NRPS); 3, SGR3239 to SGR3288 (type II PKS and NRPS); 4, SGR5914 to SGR5940 (streptomycin); 5, SGR6360 to SGR6387 (type I PKS); 6, SGR6709 to SGR6717 (NRPS). (v) Distribution of tRNA genes. (vi) Distribution of rRNA operons. (vii) G+C content percentage variation for nonoverlapping 5-kb window. Red and blue are above and below the mean, respectively. (viii) GC-skew for 3-kb window and 1-kb step. Deep pink and dark orange are above and below zero, respectively. The putative oriC gene is indicated by an arrow.
FIG. 2.
FIG. 2.
Telomere of S. griseus. (A) Comparisons of the S. griseus telomere sequence with the typical telomere sequences of seven other Streptomyces species. Conserved nucleotides among eight telomeres of the seven Streptomyces species are highlighted in light blue. Palindromes are indicated by converging arrows. Nucleotides in the possible loop of the palindromes are colored red. L and R, left and right TIRs, respectively. (B) Secondary structure of the 3′-terminal 164 nucleotides of the S. griseus chromosome predicted by the Mfold program.
FIG. 3.
FIG. 3.
Ortholog plots for S. griseus versus S. coelicolor A3(2) (A), S. griseus versus S. avermitilis (B), and S. avermitilis versus S. coelicolor A3(2) (C). Dots represent reciprocal best matches (by BLAST comparison) between orthologs. Matches on the same strand are in red, and those on the opposite strand are in blue.
FIG. 4.
FIG. 4.
DNA microarray analysis of S. griseus gene expression. (A) Scatter plot for DNA microarray analysis of S. griseus gene expression affected by the deletion of the adpA gene. The scatter plot shows the averages of normalized signal means from the wt strain and those from the ΔadpA mutant (n = 4). The red dots indicate genes that were >2-fold upregulated (P < 0.05), and the blue dots indicate genes that were >2-fold downregulated (P < 0.05) in the wt strain. (B) Comparison of results obtained by DNA microarray and quantitative RT-PCR analyses. The ratios of gene expression (wt strain to ΔadpA mutant) are plotted. The results obtained by the two methods show a high level of correlation (r2 = 0.93).
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