Streptomyces tsukubensis sp. nov., a producer of the immunosuppressant tacrolimus

Multicenter, 2-dose single-group controlled trial of tacrolimus for the severe infertility patients

INTRODUCTION

Infertility is estimated to affect 8% to 12% of reproductive-aged couples worldwide. While approximately 85% of infertile couples have an identified cause, the remaining 15% suffer physically and emotionally from unexplained intractable infertility. In recent years, maternal-to-fetal immunological abnormalities have attracted attention as mechanisms that differ from the conventional factors contributing to infertility and pregnancy loss. A T-helper 2 (Th2)-dominant immune state has been proposed as a maternal immune alteration to eliminate rejection and induce tolerance to a semi-allogeneic fetus. An imbalance in Th1 responses would not induce adequate maternal immune tolerance to the fetus or early embryos. Tacrolimus, widely used as an immunosuppressant agent in solid organ transplant recipients, is expected to suppress maternal rejection and promote tolerance to early embryos after assisted reproductive technology by modulating the immunological environment of the preimplantation endometrium. We planned an exploratory clinical trial to determine the efficacy, safety, and dosage of tacrolimus in women with intractable infertility.

METHODS AND ANALYSIS

This is a multicenter, 2-dose, single-group controlled trial in infertile women who failed to achieve a chemical pregnancy despite multiple in vitro fertilization (IVF) and embryo transfer (ET) treatment cycles. The following 2 key selection criteria were set: no underlying factors of infertility despite appropriate evaluation and presence of Th1-dominant immune state, defined as a Th1/Th2 cell ratio ≥ 10.3 in the peripheral blood. A total of 26 eligible participants are randomly assigned (in a 2:1 ratio) to receive immunosuppressive therapy with oral tacrolimus at a daily dose of 2 mg or 4 mg. Tacrolimus is administered for 16 days starting from 2 days before ET. The primary endpoint is the presence of clinical pregnancy 3 weeks after IVF/ET treatment, and the secondary endpoint is the presence of biochemical pregnancy 2 weeks after IVF/ET treatment. Safety evaluation and biomarker discovery for tacrolimus treatment in infertile women will be conducted simultaneously.

TRIAL REGISTRATION NUMBER

Japan Registry of Clinical Trials (jRCT; jRCTs031220235).

Streptomyces: The biofactory of secondary metabolites

Natural products derived from microorganisms serve as a vital resource of valuable pharmaceuticals and therapeutic agents. Streptomyces is the most ubiquitous bacterial genus in the environments with prolific capability to produce diverse and valuable natural products with significant biological activities in medicine, environments, food industries, and agronomy sectors. However, many natural products remain unexplored among Streptomyces. It is exigent to develop novel antibiotics, agrochemicals, anticancer medicines, etc., due to the fast growth in resistance to antibiotics, cancer chemotherapeutics, and pesticides. This review article focused the natural products secreted by Streptomyces and their function and importance in curing diseases and agriculture. Moreover, it discussed genomic-driven drug discovery strategies and also gave a future perspective for drug development from the Streptomyces.

Streptomyces tsukubensis VKM Aс-2618D-an Effective Producer of Tacrolimus

The Streptomyces sp. VKM Ac-2618D strain has been identified, and its morphological and physiological features have been studied in relation to the production of the immunosuppressant tacrolimus. The phenotypic variability of the strain was analyzed, and a dissociant with a high level of tacrolimus production was selected. Based on a comprehensive study of morphological, physiological, and chemotaxonomic properties and on phylogenetic analysis, the strain was named Streptomyces tsukubensis VKM Ac-2618D. The strain genome contains the full version of the tacrolimus biosynthetic gene cluster. The advantages of fed-batch cultivation mode for tacrolimus biosynthesis are shown. The results broaden the understanding of the characteristics of polyketide biosynthesis and can be used in the development of technology for tacrolimus production.

Proposal of Streptomyces aureorectus (ex Taig et al. 1969) Taig and Solovieva 1986 as a later heterotypic synonym of Streptomyces calvus Backus et al. 1957 (Approved Lists 1980) on the basis of a polyphasic taxonomic approach

As two separate genomic species, Streptomyces calvus and Streptomyces aureorectus were approved in 1980 and 1986, respectively. However, recently, it has been found that the average nucleotide identity and digital DNA-DNA hybridization values between S. calvus JCM 4326^T and S. aureorectus DSM 41692^T were 99.19 and 92.70 %, respectively, much higher than 95-96 and 70  % cut-off points proposed and the generally accepted species boundaries. These data indicated that they should be classified as the same genomic species. Furthermore, this result was also supported by a comprehensive comparison of phenotypic, chemotaxonomic and physio-biochemical characteristics between the two type strains. All these data indicated that S. calvus and S. aureorectus had the same taxonomic position. In accordance with the principle of priority, it is proposed that S. aureorectus is a later heterotypic synonyms of S. calvus.

Comparative analysis of the relationship between translation efficiency and sequence features of endogenous proteins in multiple organisms

The translation efficiency of protein genes is known to be affected by sequence features. Previous studies have found that various sequence features based on codon usage and mRNA secondary structure contribute to translation efficiency. However, most studies have focused on a specific organism, usually a model organism such as Escherichia coli or Saccharomyces cerevisiae. Here, we investigate whether the relationship between translation efficiency and sequence features is conserved among multiple organisms using publicly available ribosome profiling data and RNA-Seq data. We analyze nine organisms from various taxa: Staphylococcus aureus, five species of Streptomyces, two strains of E. coli, and S. cerevisiae. We reveal that the relationship between translation efficiency and sequence features differs across organisms, partly reflecting their taxonomy. The codon adaptation index shows high correlation in all analyzed organisms. Our study provides an insight into the diversity and commonality of sequence determinants of protein expression in these organisms.

Streptomyces qinzhouensis sp. nov., a mangrove soil actinobacterium

A novel Streptomyces strain (SSL-25T) was isolated from mangrove soil sampled at QinzhouBay, PR China. The isolate was observed to be Gram-stain-positive and to form greyish-white aerial mycelia that differentiated into straight spore chains with smooth-surfaced spores on International Streptomyces Project 2 medium. The cell-wall peptidoglycan was determined to contain ll-diaminopimelicacid. The cell-wall sugars were glucose and mannose. The predominant menaquinones were MK-9 (H6), MK-9 (H8) and MK-9 (H4). The major polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and several unidentified phospholipids. The predominant cellular fatty acids were C16:0, iso-C16:0 and summed feature 3 (C16:1ω7c/C16:1ω6c). The genome size of strain SSL-25T was 8.1 Mbp with a G+C content of 71.5 mol%. Phylogenetic analysis indicated that strain SSL-25T is closely related to Streptomyces tsukubensis NRRL 18488T (99.4 % sequence similarity). However, the digital DNA–DNA hybridization (39.8 %) and average nucleotide identity (91.3 %) values between them showed that it represents a distinct species. Furthermore, the results of morphological, physiological and biochemical tests allowed further phenotypic differentiation of strain SSL-25T from S. tsukubensis NRRL 18488T. Therefore, based on these results, it is concluded that strain SSL-25T represents a novel Streptomyces species, for which the name Streptomyces qinzhouensis sp. nov. is proposed. The type strain is SSL-25T (=CICC 11054T=JCM33585T).

Streptomyces cadmiisoli sp. nov., a novel actinomycete isolated from cadmium-contaminated soil

A novel Streptomyces strain, ZFG47T, isolated from a cadmium-contaminated soil sample, was taxonomically studied in detail. Strain ZFG47T formed long, flexuous spiral spore chains consisting of elliptoid spores with spiny surfaces. The cell-wall hydrolysates contained ll-diaminopimelic acid as the diagnostic diamino acid. The major menaquinones consisted of MK-9(H2), MK-9(H4) and MK-9(H8). The major polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol mannosides. The predominant cellular fatty acids were iso-C16 : 0, C16 : 0 and anteiso-C15 : 0. The 16S rRNA gene sequence-based phylogenetic analysis indicated that this strain belongs to the genus Streptomyces , showing the highest sequence similarity to Streptomyces koyangensis VK-A60T (98.7 %). However, the digital DNA–DNA hybridization value, the average nucleotide identity value and the MLSA evolutionary distance between this strain and S. koyangensis VK-A60T showed that it belonged to a distinct species. Furthermore, the novel isolate could be distinctly differentiated from S. koyangensis VK-A60T by morphological, physiological and biochemical characteristics. On the basis of the evidence from this polyphasic study, it is concluded that strain ZFG47T represents a novel species of the genus Streptomyces , for which the name Streptomyces cadmiisoli sp. nov. is proposed, with strain ZFG47T (CICC 11050T=JCM 32897T) as the type strain.

Analysis and validation of the pho regulon in the tacrolimus-producer strain Streptomyces tsukubaensis: differences with the model organism Streptomyces coelicolor

Inorganic and organic phosphate controls both primary and secondary metabolism in Streptomyces genus. Metabolism regulation by phosphate in Streptomyces species is mediated by the PhoR-PhoP two-component system. Response regulator PhoP binds to conserved sequences of 11 nucleotides called direct repeat units (DRus), whose organization and conservation determine the binding of PhoP to distinct promoters. Streptomyces tsukubaensis is the industrial producer of the clinical immunosuppressant tacrolimus (FK506). A bioinformatic genome analysis detected several genes with conserved PHO boxes involved in phosphate scavenging and transport, nitrogen regulation, and secondary metabolite production. In this article, the PhoP regulation has been confirmed by electrophoretic mobility shift assays (EMSA) of the most relevant members of the traditional pho regulon such as the two-component system PhoR-P or genes involved in high-affinity phosphate transport (pstSCAB) and low-affinity phosphate transport (pit). However, the PhoP control over phosphatase genes in S. tsukubaensis is significantly different from the pattern reported in the model bacteria Streptomyces coelicolor. Thus, neither the alkaline phosphatase PhoA nor PhoD is regulated by PhoP. On the contrary, the binding of PhoP to the promoter of a novel putative phosphatase PhoX was confirmed. A crosstalk of the PhoP and GlnR regulators, which balances phosphate and nitrogen utilization, also occurs in S. tsukubaensis but slightly modified. Finally, PhoP regulates genes, like afsS, that link phosphate control and secondary metabolite production in S. tsukubaensis. In summary, there are notable differences between the regulation of specific genes of the pho regulon in S. tsukubaensis and the model organism S. coelicolor.

Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters among taxonomically close Streptomyces strains

To identify the species of butyrolactol-producing Streptomyces strain TP-A0882, whole genome-sequencing of three type strains in a close taxonomic relationship was performed. In silico DNA-DNA hybridization using the genome sequences suggested that Streptomyces sp. TP-A0882 is classified as Streptomyces diastaticus subsp. ardesiacus. Strain TP-A0882, S. diastaticus subsp. ardesiacus NBRC 15402T, Streptomyces coelicoflavus NBRC 15399T, and Streptomyces rubrogriseus NBRC 15455T harbor at least 14, 14, 10, and 12 biosynthetic gene clusters (BGCs), respectively, coding for nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). All 14 gene clusters were shared by S. diastaticus subsp. ardesiacus strains TP-A0882 and NBRC 15402T, while only four gene clusters were shared by the three distinct species. Although BGCs for bacteriocin, ectoine, indole, melanine, siderophores such as deferrioxamine, terpenes such as albaflavenone, hopene, carotenoid and geosmin are shared by the three species, many BGCs for secondary metabolites such as butyrolactone, lantipeptides, oligosaccharide, some terpenes are species-specific. These results indicate the possibility that strains belonging to the same species possess the same set of secondary metabolite-biosynthetic pathways, whereas strains belonging to distinct species have species-specific pathways, in addition to some common pathways, even if the strains are taxonomically close.

Trends in the biosynthesis and production of the immunosuppressant tacrolimus (FK506)

The current off-patent state of tacrolimus (FK506) has opened the hunting season for new generic pharmaceutical formulations of this immunosuppressant. This fact has boosted the scientific and industrial research on tacrolimus for the last 5 years in order to improve its production. The fast discovery of tacrolimus producer strains has generated a huge number of producers, which presents the biosynthetic cluster of FK506 as a high promiscuous genetic region. For the first time, the current state-of-the-art on the tacrolimus biosynthesis, production improvements and drug purification is reviewed. On one hand, all the genes involved in the tacrolimus biosynthesis, in addition to the traditional PKS/NRPS, as well as their regulation are analysed. On the other hand, tacrolimus direct and indirect precursors are reviewed as a straight manner to improve the final yield, which is a current trend in the field. Twenty years of industrial and scientific improvements on tacrolimus production are summarised, whereas future trends are also drafted.

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.