STREPTObook
Introduction
As the starting point of our project, we fancied the production of antibiotics from Streptomyces strains that could fix atmospheric CO2. We naturally had two ways to complete this project. Either we used a strain that could fix carbon and we made it produce antibiotics, or we had to pick a strain that could produce antibiotics and make it fix atmospheric CO2.
Since both approaches can be interesting, we decided to characterize several strains to start a ‘chassis registry’ which could be useful both for our project but perhaps also for other projects based on the use of Streptomyces by future iGEMers! To do this, we needed standardized protocols, both to carry out phenotype analysis (growth, antibiotic production) and genotype analysis (coding potential in terms of specialized metabolites, possible presence of prophages that could be detrimental to industrial production by the strains, sites for specific vector integration, etc.).
Actually, handling Streptomyces in laboratories is extremely hard without the proper knowledge. Recognizing them, taking care of the renewal of the spore stocks etc. requires skills. Thanks to the advice from our coaches we could take on such challenges.
While we could get guidance when we needed it, not all iGEM teams will be lucky enough to have someone that can help them overcome such problems. Therefore, at team GO_Paris-Saclay, we decided to create a comprehensive documentation compiling all the protocols that we used to take care of our strains, how to analyze Streptomyces genomes, analyses we performed throughout the year, and which strain we considered to be the best to carry on our project.
We sincerely wish that this contribution will motivate future iGEM teams to use this fancy chassis and further increase the chassis diversity within the iGEM competition.
The complete STREPTObook with all protocols, strain comparison and bioinformatics analyses can be downloaded here:
More information about the chassis experiments and results can be found here.
Please find below a strain-by-strain description of seven Streptomyces strains of interest that competed with us in iGEM!
Legend of the table:
aSMBGCs (specialized metabolite biosynthetic gene clusters) were predicted using AntiSMASH 6.0.
bGeneration time was determined in exponential phase after inoculating 106 spores in 10 ml of MP5 medium at 30°C under a regular atmosphere. Color code: the bluer, the shorter; the redder, the longer
cLag phase in MP5 (as described in b) as considered as short if < 12h (blue), or long if > to 12 h (red).
dThe biomass (wet weight) was measured after 5 days of growth as described in [b].
eAntibacterial efficiency (ABE) (defined as the size in cm of the halo of inhibition of Micrococcus luteus growth) was determined after 3 days of growth as described in [b]. Antibiotic production (defined as the size in cm of the halo of inhibition of M. luteus growth) was determined after inoculating 5.106 spores on MP5 solid medium, and growth during 3 days at 30°C under a regular atmosphere.
fABE was determined after inoculating 5.106 spores on sub minimal medium devoid of carbon source solid medium, and growth during 3 days at 30°C under a regular atmosphere.
gABE was determined after inoculating 5.106 spores on minimal medium containing 0.5 % glycerol (an industrial waste) devoid of carbon source solid medium, and growth during 3 days at 30°C under a regular atmosphere.
hThe conjugation was performed for all strains in conditions optimized for Streptomyces ambofaciens engineering (page 11 of the STREPTObook).
> Streptomyces albidoflavus
Short Description
S. albidoflavus, is a species of Streptomyces extracted from the surface layers of Polish soil and named by Dr. Waksman in 1948 ‘S. albus’. Its name changed to S. albidoflavus in 2018. Its genome, at 6.8 Mb in length, is among the smallest in the Streptomyces genus. Its genome tends to have a reduced number of duplicated genes. S. albidoflavus has been repeatedly proposed as one of the best chassis for heterologous SMBGC expression, notably because of its fast growth and limited production of endogenous specialized metabolites.
Figures: bottom-left: Picture taken with a microscope using a Prime BSI Scientific CMOS (sCMOS) camera; bottom-right: Picture of colonies grown on MP5 solid medium
| Genome Analysis | |
|---|---|
Chromosome Accession Number | NZ_CP059254 |
| Plasmid □ Yes ⌧ No Accession number(s) if appropriated | |
| Size (bp) | Chromosome: 6942952 bp Plasmid: - bp |
| Position of the origin of replication (dnaA gene start position) | 3467688 |
| GC% | Chromosome: 73.3 Plasmid: - bp |
| Number of coding sequences | Chromosome: 5836 Plasmid: - |
| Pseudogenes | Chromosome: 101 Plasmid: - |
| Number of ribosomal RNA genes (16S, 23S, 5S) | Chromosome: 21 genes (7 operons) Plasmid: - |
| Number of transfer RNA genes | Chromosome: 69 Plasmid: - |
| Number of SMBGCs² | 25 |
| SMBGCs encoded with high similarity with known clusters | Antibiotics: lanthipeptide (SAL-2242) Antifungi: Antimycin Others: hopene, geosmine, surugamide A / surugamide D, desferrioxamin B, ectoine, indigoidine, candicidin |
| Prophage prediction | Intact: - Questionable: - Incomplete: 3 (2918405-2926554, 71.34%), (3214020-3219014, 57.16%), (3556609-3561603, 57.16%) |
- attb sites of interest performed on NZ_CP059254 sequence.
attB-PhiC31: □ Yes ⌧ No
Start: -
End: -
Coverage: - %
Identities: - %
Gene name: -
Predicted function: -
attB-PhiBT1: □ Yes ⌧ No
Start: -
End: -
Coverage: - %
Identities: - %
Gene name: -
Predicted function: -
attB-pSAM2: ⌧ Yes □ No
Start: 3117170
End: 3117195
Coverage: 100 %
Identities: 100 %
Gene name: XNRR2_RS13665
Predicted function: tRNA-Pro
attB-VWB: ⌧ Yes □ No
Start: 2548667
End: 2548711
Coverage: 100 %
Identities: 100 %
Gene name: XNRR2_RS10875
Predicted function: tRNA-Arg
attB-R4: ⌧ Yes □ No
Start: 755887
End: 755931
Coverage: 45/50 (90 %)
Identities: 43/45 (96 %)
Gene name: XNRR2_RS03210
Predicted function: AMP-binding protein
attB-TG1: ⌧ Yes □ No
Start: 3739865
End: 3739824
Coverage: 42/50 (84 %)
Identities: 39/42 (93 %)
Gene name: XNRR2_RS16415
Predicted function: pyridoxal phosphate-dependent aminotransferase
attB-PhiJoe ⌧ Yes □ No
Start: 5046297
End: 5046251
Coverage: 47/50 (94%)
Identities: 42/47 (89%)
Gene name: XNRR2_RS22120
Predicted function: B12-binding radical SAM domain protein
attB-SV1: □ Yes ⌧ No (too truncated, may not be functional)
Start: 981405
End: 981389
Coverage: 17/50
Identities: 17/17 (83%)
Gene name: XNRR2_RS04170
Predicted function: L-lactate permease
> Streptomyces ambofaciens
Short Description
S. ambofaciens was isolated from a soil sample in the Somme department in France by Mrs. S. Pinnert-Sindico in the early 1950s. From liquid cultures of this species, two antibiotics were identified very early on: spiramycin, discovered this way, and
congocidine, already known. The species name 'ambofaciens' ('doing two things') was then given to it. The strain has since been used for the industrial production of spiramycin, an antibiotic given to pregnant women and used to combat toxoplasmosis. Congocidine, also known as netropsin, is an antibacterial that binds in the small groove of DNA to specific sequences (a sequence of 4 or more AT bases) and has antibacterial, antiviral and antitumour activity, but is far too toxic for therapeutic use. S. ambofaciens ATCC 23877 also produces kinamycin (it has two clusters directing production), antimycin and stambomycin.
Figures: bottom-left: Picture taken with a microscope using a Prime BSI Scientific CMOS (sCMOS) camera; bottom-right: Picture of colonies grown on MP5 solid medium
| Genome Analysis | |
|---|---|
Chromosome Accession Number | NZ_CP012382.1 |
| Plasmid Accession number(s) if appropriated | NZ_CP012383.1 (pSAM1) circular plasmid Please note that this strain also has an integrative plasmid (pSAM2 at position: 4319471 - 4330473) near the chromosomal origin of replication |
| Size (bp) | Chromosome: 8303940 bp, including TIRs (196959 bp on each side) Plasmid (pSAM1): 89658 bp |
| Position of the origin of replication (dnaA gene start position) | 4021374 |
| GC% | Chromosome: 72.2 Plasmid (pSAM1): 69.2 bp |
| Number of coding sequences | Chromosome: 7090 Plasmid (pSAM1): 127 |
| Pseudogenes | Chromosome: 211 Plasmid: 4 |
| Number of ribosomal RNA genes (16S, 23S, 5S) | Chromosome: 17 genes (6 operons including one incomplete operon) Plasmid (pSAM1): - |
| Number of transfer RNA genes | Chromosome: 72 Plasmid (pSAM1): - |
| Number of SMBGCs² | 27 |
| SMBGCs encoded with high similarity with known clusters | Antibiotics: Spiramycin, netropsin/congocidine, kanamycin, lanthipeptide Antifungi: Antimycin Anticancer: Stambomycins Others: Ectoin, melanin, desferrioxamins, albaflavenone, geosmin, hopene, coelichelin |
| Prophage prediction | Intact: 1 (region: 6575622-6650598 ; 66.38 GC%) Questionable: - Incomplete: - |
- attb sites of interest performed on NZ_CP012382.1 sequence.
attB-PhiC31: ⌧ Yes □ No
Start: 4110202
End: 4110152
Coverage: 100 %
Identities: 100 %
Gene name: SAM23877_3857
Predicted function: Chromosome condensation protein
attB-PhiBT1: ⌧ Yes □ No
Start: 4941593
End: 4941558
Coverage: 100 %
Identities: 100 %
Gene name: SAM23877_4663
Predicted function: Putative integral membrane protein
attB-pSAM2: ⌧ Yes □ No
Start: 4330483
End: 4330458
Coverage: 100 %
Identities: 100 %
Gene name: SAM23877_tRNA51
Predicted function: tRNA-Pro
attB-VWB: ⌧ Yes □ No Two sites!
First site:
Start: 3474165
End: 3474209
Coverage: 100 %
Identities: 100 %
Gene name: SAM23877_tRNA15
Predicted function: tRNA-Arg
Second site:
Start: 3483545
End: 3483587
Coverage: 95.6 % (43/45 bp)
Identities: 100 %
Gene name: SAM23877_tRNA16
Predicted function: Pseudo-tRNA
attB-R4: ⌧ Yes □ No There is just half a site
Start: 6424241
End: 6424212
attB-TG1: ⌧ Yes □ No (but degenerated)
Start: 4110202
End: 4110152
Coverage: 94 % (47/50 bp)
Identities: 85 %
Gene name: SAM23877_3963
Predicted function: putative N-succinyldiaminopimelate aminotransferase DapC
attB-PhiJoe ⌧ Yes □ No (but degenerated)
Start: 2783791
End: 2783840
Coverage: 100 %
Identities: 84 %
Gene name: SAM23877_2652
Predicted function: Hypothetical protein
attB-PhiBT1: ⌧ Yes □ No
Start: 3555856
End: 3555910
Coverage: 100 %
Identities: 91 %
Gene name: SAM23877_3343
Predicted function: 4-coumarate:CoA ligase
> Streptomyces bottropensis
Short Description
S. bottropensis ATCC 25435 is the central strain of our project. Although still very poorly known, it is nevertheless used for its biosynthesis of an antibiotic, bottromycin. It has an 18 kb GC-rich genomic island of unknown origin containing the genes encoding a class I RuBisCO and PKR, making it a CO2-fixing module. As the functioning of the gene regulatory system of this island is still unknown, this strain has the potential to be the first C-autotrophic Streptomyces species using a RuBisCO for carbon fixation. Of note, some strains of S. bottropensis can cause common potato scab, a disease that does not affect humans but has caused economic disasters in the past.
Figures: bottom-left: Picture taken with a microscope using a Prime BSI Scientific CMOS (sCMOS) camera; bottom-right: Picture of colonies grown on MP5 solid medium
| Genome Analysis (This genome is just a draft!) | |
|---|---|
Chromosome Accession Number | NZ_KB911581.1 |
| Plasmid □ Yes ⌧ No Accession number(s) if appropriated | |
| Size (bp) | Chromosome: 8 955 726 bp (Ungapped length: 8,955,426 bp) - Please note that this is a draft genome Plasmid: - |
| Position of the origin of replication (dnaA gene start position) | 277 |
| GC% | Chromosome: 71.2 % Plasmid: - |
| Number of coding sequences | Chromosome: 7516 Plasmid: - |
| Pseudogenes | Chromosome: 302 Plasmid: - |
| Number of ribosomal RNA genes (16S, 23S, 5S) | Chromosome: 18 genes (6 operons) Plasmid: - |
| Number of transfer RNA genes | Chromosome: 68 Plasmid: - |
| Number of SMBGCs² | 30 |
| SMBGCs encoded with high similarity with known clusters | Antibiotics:bottromycin, informatipeptin (lanthipeptide) Antifungi: - Others: Ectoin, spore pigment, geosmin, scabichelin, hopene, desferrioxamin B / desferrioxamine E |
| Prophage prediction | Intact: - Questionable: 1 (5445527-5475575, 66.55%) Incomplete: 4 (region: 2197364-2207566; 69.04 GC%) (region: 2985585-3018597 ; 69.52 GC%) (region: 5548994-5560170; 66.82 GC%) (region: 5564717-5585490; 69.11 GC%) |
- attb sites of interest
attB-PhiC31: □ Yes ⌧ No
Start: -
End: -
Coverage: - %
Identities: - %
Gene name: -
Predicted function: -
attB-PhiBT1: □ Yes ⌧ No
Start: -
End: -
Coverage: - %
Identities: - %
Gene name: -
Predicted function: -
attB-pSAM2: ⌧ Yes □ No
Start: 584877
End: 584852
Coverage: 26/26 (100 %)
Identities: 100 %
Gene name: STRBO_RS0102645
Predicted function: tRNA-Pro
attB-VWB: ⌧ Yes □ No
Start: 8249725
End: 8249769
Coverage: 100 %
Identities: 100 %
Gene name: STRBO_RS0136405
Predicted function: tRNA-Arg
attB-R4: ⌧ Yes □ No
Start: 2701461
End: 2701504
Coverage: 44/50 (88%)
Identities: 42/44 (95%)
Gene name: STRBO_RS0111835
Predicted function: AMP-binding protein
attB-TG1: ⌧ Yes □ No
Start: 469563
End: 469523
Coverage: 41/50 (82 %)
Identities: 40/41 (98%)
Gene name: STRBO_RS0102155
Predicted function: pyridoxal phosphate-dependent aminotransferase
attB-PhiJoe □ Yes ⌧ No (too truncated, may not be functional)
Start: 346819
End: 346801
Coverage: 19/50 (38%)
Identities: 18/19 (95%)
Gene name: -
Predicted function: -
attB-SV1: ⌧ Yes □ No
Start: 8392633
End: 8392684
Coverage: 50/55 (91 %)
Identities: 50/52 (96%)
Gene name: STRBO_RS0137120
Predicted function: 4-coumarate--CoA ligase family protein
> Streptomyces coelicolor
Short Description
S. coelicolor is the best characterised Streptomyces species. S. coelicolor is a filamentous gram-positive bacterium discovered in 1908 by R. Muller on a potato. It was first given the name Streptothrix coelicolor by Muller and later adopted the name it has today. S. coelicolor was sequenced by the John Innes Center and the Sanger Institute following extensive studies by David A Hopwood. Like the other strains of the genus, S. coelicolor lives in the surface strains of the soil and is responsible for some of the decomposition of organic matter in the soil. This species is well known for its characteristic blue and/or red colonies. It produces actinorhodin (blue) and undecylprodigiosin (red).
Figures: bottom-left: Picture taken with a microscope using a Prime BSI Scientific CMOS (sCMOS) camera; bottom-right: Picture of colonies grown on MP5 solid medium
| Genome Analysis | |
|---|---|
Chromosome Accession Number | NC_003888.3 |
| Plasmid ⌧ Yes □ No Accession number(s) if appropriated | 2 : SCP1 SCP2 |
| Size (bp) | Chromosome: 8 667 507 bp Plasmid: SCP1 (NC_003903.1): 356 023 bp SCP2 (NC_003904.1) : 31 317 bp |
| Position of the origin of replication (dnaA gene start position) | 4270778 |
| GC% | Chromosome: 72.1% Plasmid: SCP1: 69.1% SCP2: 72.1% |
| Number of coding sequences | Chromosome: 7 769 Plasmid: SCP1 : 351 SCP2 : 34 |
| Pseudogenes | Chromosome: 56 Plasmid: SCP1 : 5 SCP2 : - |
| Number of ribosomal RNA genes (16S, 23S, 5S) | Chromosome: 18 genes (6 operons) Plasmid: - |
| Number of transfer RNA genes | Chromosome: 65 Plasmid: - |
| Number of SMBGCs² | 27 |
| SMBGCs encoded with high similarity with known clusters | Antibiotics: coelibactin, CDA1b/CDA2a/CDA2b/CDA3a/CDA3b/CDA 4a/CDA4b, actinorhodin, undecylprodigiosin, lanthipeptide SapB, coelimycin P1 Antifungi: - Others: isorenieratene, ectoine, desferrioxaminB/ desferrioxaminE, albaflavenone, geosmin, hopene, arsono- polyketide, germicidin, coelichelin |
| Prophage prediction | Intact: - Questionable: - Incomplete: 3 (region: 3227050-3236339; 71.51% GC) (region: 5178021-5186988 71.77% GC) (region: 5947312-5954361; 71.50% GC); |
- attb sites of interest (performed on NC_003888.3 sequence)
attB-PhiC31: ⌧ Yes □ No
Start: 4178697
End: 4178747
Coverage: 100 %
Identities: 100 %
Gene name: SCO3798
Predicted function: chromosome condensation protein
attB-PhiBT1: ⌧ Yes □ No
Start: 5279940
End: 5279905
Coverage: 100 %
Identities: 100 %
Gene name: SCO4848
Predicted function: hypothetical protein
attB-pSAM2: ⌧ Yes □ No
Start: 3963133
End: 3963158
Coverage: 100 %
Identities: 100 %
Gene name: SCOt29
Predicted function: tRNA-Pro
attB-VWB: ⌧ Yes □ No
Start: 3602638
End: 3602682
Coverage: 100 %
Identities: 100 %
Gene name: SCOt27
Predicted function: tRNA-Arg
attB-R4: ⌧ Yes (but degenerated) □ No
Start: 6806602
End: 6806559
Coverage: 44/50 (88%)
Identities: 40/44 (91%)
Gene name: SCO6196
Predicted function: AMP-binding protein
attB-TG1: ⌧ Yes (but degenerated) □ No
Start: 4037412
End: 4037446
Coverage: 35/50 (70 %)
Identities: 31/35 (89%)
Gene name: SCO3658
Predicted function: aminotransferase
attB-PhiJoe □ Yes ⌧ No (only half a site)
Start: 2827472
End: 2827497
Coverage: 26/50 ( 52 %)
Identities: 26/26 (100%)
Gene name: SCO2606
Predicted function: hypothetical protein
attB-SV1: ⌧ Yes □ No
Start: 4800590
End: 4800536
Coverage: 100 %
Identities: 54/55(98%)
Gene name: SCO4383
Predicted function: 4-coumarate--CoA ligase family protein
> Streptomyces lividans
Short Description
This strain is very similar to S. coelicolor A3 (2) which was discovered in 1965, but produces much lower antibiotics than this strain. It is very well characterized, and therefore widely used as a heterologous producer of SMBGCs.
Figures: bottom-left: Picture taken with a microscope using a Prime BSI Scientific CMOS (sCMOS) camera; bottom-right: Picture of colonies grown on MP5 solid medium
| Genome Analysis | |
|---|---|
Chromosome Accession Number | NZ_CP009124.1 |
| Plasmid □ Yes ⌧ No Accession number(s) if appropriated | - |
| Size (bp) | Chromosome: 8 345 283 bp Plasmid: - |
| Position of the origin of replication (dnaA gene start position) | 4187778 |
| GC% | Chromosome: 72.2% Plasmid: - |
| Number of coding sequences | Chromosome: 7 306 Plasmid: : - |
| Pseudogenes | Chromosome: 134 Plasmid: - |
| Number of ribosomal RNA genes (16S, 23S, 5S) | Chromosome: 18 genes (6 operons) Plasmid: - |
| Number of transfer RNA genes | Chromosome: 66 Plasmid: - |
| Number of SMBGCs² | 27 |
| SMBGCs encoded with high similarity with known clusters | Antibiotics: coelibactin, undecylprodigiosin, Actinorhodin, CDA1b/CDA2a/CDA2b/CDA3a/CDA3b/CDA 4a/CDA4b, SapB lanthipeptide, coelimycin P1 Antifungi: - Others: germincidin, hopene, coelimycin P1, geosmin, albaflavenone, desferrioxamin B / desferrioamine E, melanin, ectoine, coelichelin, isorenieratene |
| Prophage prediction | Intact: - Questionable: - Incomplete: 1 (region : 256645-2573357 ; 71.46 GC%) |
- attb sites of interest (performed with NZ_CP009124.1 sequence)
attB-PhiC31: ⌧ Yes □ No
Start: 4 287 002
End: 4 286 952
Coverage: 100 %
Identities: 100 %
Gene name: SLIV_19310
Predicted function: chromosome condensation protein
attB-PhiBT1: ⌧ Yes □ No
Start: 3 212 063
End: 3 212 098
Coverage: 100 %
Identities: 100 %
Gene name: SLIV_14132
Predicted function: hypothetical protein
attB-pSAM2: ⌧ Yes □ No
Start: 4 502 043
End: 4 502 018
Coverage: 100 %
Identities: 100 %
Gene name: SLIV_t20370
Predicted function: tRNA-Pro
attB-VWB: ⌧ Yes □ No
Start: 4 739 309
End: 4 739 265
Coverage: 100 %
Identities: 100 %
Gene name: SLIV_t21440
Predicted function: tRNA-Arg
attB-R4: ⌧ Yes □ No
Start: 1 649 478
End: 1 649 521
Coverage: 44/50 (88%)
Identities: 40/44 (91%)
Gene name: SLIV_07155
Predicted function: Acetyl_CoA synthetase
attB-TG1: ⌧ Yes (but degenerated) □ No
Start: 4 428 488
End: 4 428 454
Coverage: 35/50 (70 %)
Identities: 31/35 (89%)
Gene name: SLIV_RS20010
Predicted function: pyridoxal phosphate-dependent aminotransferase
attB-PhiJoe ⌧ Yes (but very degenerated) □ No
Start: 5 506 298
End: 5 506 273
Coverage: 26/50 ( 52 %)
Identities: 26/26 (100%)
Gene name: SLIV_24645
Predicted function: TIGR03960 family B12-binding radical SAM protein
attB-SV1: ⌧ Yes (but very degenerated) □ No
Start: 3 701 673
End: 3 701 727
Coverage: 100 %
Identities: 54/55(98%)
Gene name: SLIV_16515
Predicted function: putative 4-coumarate-CoA ligase
> Streptomyces rimosus
Short Description
S. rimosus is a species of Streptomyces from the surface layers of the soil. It has been known since 1950 for its production of oxytetracycline but produces many other tetracyclines.
Figures: bottom-left: Picture taken with a microscope using a Prime BSI Scientific CMOS (sCMOS) camera; bottom-right: Picture of colonies grown on MP5 solid medium
| Genome Analysis | |
|---|---|
Chromosome Accession Number | NZ_CP048261.1 |
| Plasmid ⌧ Yes □ No Accession number(s) if appropriated | NZ_CP048262.1 (pSRP1) linear plasmid |
| Size (bp) | Chromosome: 9 351 267 bp Plasmid (pSRP1): 292 624 bp |
| Position of the origin of replication (dnaA gene start position) | 4 728 560 |
| GC% | Chromosome: 72.0% Plasmid (pSRP1): 69.6% |
| Number of coding sequences | Chromosome: 7 906 Plasmid (pSR1): 260 |
| Pseudogenes | Chromosome: 202 Plasmid (pSR1): 25 |
| Number of ribosomal RNA genes (16S, 23S, 5S) | Chromosome: 21 genes (7 operons) Plasmid (pSR1): - |
| Number of transfer RNA genes | Chromosome: 68 Plasmid (pSR1): - |
| Number of SMBGCs² | 42 |
| SMBGCs encoded with high similarity with known clusters | Antibiotics: oxytetracycline, SAL-2242 lanthipeptide Antifungi: - Others: Deferoxamine, ectoin, geosmin, tyrobetaine, isocomplestatin, hopene, rimosamide, isorenieratene |
| Prophage prediction | Intact:1 (region: 2660256 - 2727200; 70.73% GC) Questionable: - Incomplete: 2 ( region 3915919 – 3945799; 70.51% GC), (region 3954650 – 3971534; 70.54% GC) |
- attb sites of interest in NZ_CP048261.1 sequence
attB-PhiC31: ⌧ Yes □ No
Start: 4 618 357
End: 4 618 407
Coverage: 100 %
Identities: 48/51 (94%)
Gene name: SRIM_RS20750
Predicted function: pirin family protein
attB-PhiBT1: ⌧ Yes □ No
Start: 5 711 347
End: 5 711 313
Coverage: 35/36 (97.2 %)
Identities: 33/35 (94%)
Gene name: SRIM_RS42680
Predicted function: hypothetical protein
attB-pSAM2: ⌧ Yes □ No
Start: 5 094 679
End: 5 094 654
Coverage: 100 %
Identities: 100 %
Gene name: SRIM_RS23060
Predicted function: tRNA-Pro
attB-VWB: ⌧ Yes □ No
Start: 3 912 420
End: 3 912 464
Coverage: 100 %
Identities: 100 %
Gene name: SRIM_RS17305
Predicted function: tRNA-Arg
attB-R4: ⌧ Yes □ No
Start: 7 447 513
End: 7 447 466
Coverage: 48/50 (96 %)
Identities: 47/48 (98%)
Gene name: SRIM_RS32960
Predicted function: AMP-binding protein
attB-TG1: ⌧ Yes □ No
Start: 4 869 393
End: 4 869 359
Coverage: 35/50 (70 %)
Identities: 33/35 (94%)
Gene name: SRIMR7_RS20685
Predicted function: pyridoxal phosphate-dependent aminotransferase
attB-PhiJoe ⌧ Yes □ No
Start: 6 253 952
End: 6 253 906
Coverage: 47/50 (94 %)
Identities: 41/47 (87 %)
Gene name: SRIMR7_RS27065
Predicted function: TIGR03960 family B12-binding radical SAM protein
attB-SV1: ⌧ Yes □ No
Start: 5 557 219
End: 5 557 176
Coverage: 44/50 (88 %)
Identities: 42/44 (95%)
Gene name: SRIM_RS25080
Predicted function: 4-coumarate--CoA ligase family protein
> Streptomyces venezuelae
Short Description
S. venezuelae is a species of Streptomyces from the soil at Caracas (Venezuela). Please note that many strains are called ‘venezuelae’ but can be rather phylogenetically unrelated (Lorenzi et al., https://doi.org/10.1101/2022.06.23.497307). The S. venezuelae ATCC 10712 strain is a model organism, very well described (a lot of genomic data available) which has the particularity to sporulate in liquid medium. This property is very rare in Streptomyces genus. This strain has also a rather fast growth compared to others.
Figures: bottom-left: Picture taken with a microscope using a Prime BSI Scientific CMOS (sCMOS) camera; bottom-right: Picture of colonies grown on MP5 solid medium
| Genome Analysis | |
|---|---|
Chromosome Accession Number | NZ_CP029197.1 |
| Plasmid □ Yes ⌧ No Accession number(s) if appropriated | NZ_CP048262.1 (pSRP1) linear plasmid |
| Size (bp) | Chromosome: 8 223 505 bp Plasmid: - |
| Position of the origin of replication (dnaA gene start position) | 3 972 844 |
| GC% | Chromosome: 72.5% Plasmid: - |
| Number of coding sequences | Chromosome: 7 231 Plasmid: - |
| Pseudogenes | Chromosome: 128 Plasmid: - |
| Number of ribosomal RNA genes (16S, 23S, 5S) | Chromosome: 21 genes (7 operons) Plasmid: - |
| Number of transfer RNA genes | Chromosome: 70 Plasmid: - |
| Number of SMBGCs² | 31 |
| SMBGCs encoded with high similarity with known clusters | Antibiotics: venemycin, chloramphenicol, SapB lanthipeptide, venezuelin Antifungi: - Others: ectoine, geosmin, desferrioxamin B, albusnodin, A-factor, hopene, spore pigment, 2-methylisoborneol, alkylresorcinol |
| Prophage prediction | Intact: 1 (3116956-3150010 ; 71.57%) Questionable: 1 (region : 2315521- 2342618; 68.57 % GC) Incomplete: 2 (region: 2285228-2298103; 70.44%GC) ( region: 4698282-4724275; 70.33% GC) |
- attb sites of interest performed on NZ_CP029197.1 sequence
attB-PhiC31: ⌧ Yes □ No
Start: 3 879 114
End: 3 879 164
Coverage: 100 %
Identities: 49/51(96%)
Gene name: DEJ43_RS17755
Predicted function: pirin family protein
attB-PhiBT1: □ Yes ⌧ No
Start: -
End: -
Coverage: -
Identities: -
Gene name: -
Predicted function: -
attB-pSAM2: ⌧ Yes □ No
Start: 3 675 733
End: 3 675 758
Coverage: 100 %
Identities: 100 %
Gene name: DEJ43_RS16720
Predicted function: tRNA-Pro
attB-VWB: ⌧ Yes □ No
Start: 3 366 270
End: 3 366 314
Coverage: 100 %
Identities: 100 %
Gene name: DEJ43_RS15285
Predicted function: tRNA-Arg
attB-R4: ⌧ Yes □ No
Start: 6 619 143
End: 6 619 180
Coverage: 38/50 (76%)
Identities: 38/38 (100%)
Gene name: DEJ43_RS30450
Predicted function: AMP-binding protein
attB-TG1: ⌧ Yes □ No
Start: 3 742 514
End: 3 742 548
Coverage: 35/50 (70 %)
Identities: 31/35 (89%)
Gene name: DEJ43_RS17050
Predicted function: pyridoxal phosphate-dependent aminotransferase
attB-PhiJoe ⌧ Yes □ No
Start: 2 582 843
End: 2 582 892
Coverage: 100%
Identities: 100%
Gene name: DEJ43_RS11810
Predicted function: TIGR03960 family B12-binding radical SAM protein
attB-SV1: ⌧ Yes (but degenerated) □ No
Start: 1 006 802
End: 1 006 773
Coverage: 30/55 (54.5%)
Identities: 27/30 (90%)
Gene name: DEJ43_RS04275
Predicted function: long-chain fatty acid--CoA ligase