METTL9 derived circular RNA circ-METTL9 sponges miR-551b-5p to accelerate colorectal cancer progression by upregulating CDK6.

Circular RNAs (circRNAs) have been accepted to play key roles in the development and progression of mutiple cancers including colorectal cancer (CRC). Here, we identified circ-METTL9, derived from 2 to 4 exons of METTL9 gene, may promote CRC progression by accelerating cell cycle progression. However, the role and mechanism of circ-METTL9 in CRC remains unclear. Based on our data, the expression of circ-METTL9 was significantly upregulated in CRC tissues and markedly increased in advanced tumors in CRC patients. Functional experiments demonstrated that circ-METTL9 overexpression promoted CRC cells proliferation and migration in vitro, and simultaneously enhanced CRC tumor growth and metastasis in vivo. Mechanistically, RNA immunoprecipitation (RIP) assays proved that circ-METTL9 might be a miRNA sponge, and RNA pulldown assays showed the interaction between circ-METTL9 and miR-551b-5p. Notably, cyclin-dependent kinase 6 (CDK6), a key regulator in cell cycle, is a conserved downstream target of miR-551b-5p. Taken together, our findings highlight a novel oncogenic function of circ-METTL9 in CRC progression via circ-METTL9/miR-551b-5p/CDK6 axis, which may serve as a prognostic biomarker and therapeutic target for CRC patients.

[Identification of active components of Dendrobium inhibit growth of gastric cancer cells based on component-activity relationship].

Three cancer cell lines including gastric cancer SGC-7901, HGC-27, and MGC-803 cells were employed to evaluate the bioactivity of seven Dendrobium species. Simultaneously, these Dendrobium species were assessed with UPLC-Q-TOF-MS, and 504 common peaks were found. Based on the hypothesis that biological effects varied with differences in components, multivariate relevance analysis for chemical component-activity relationship of Dendrobium, including grey relation(GRA) and partial least squares(PLS) analysis were performed to evaluate the contribution of each identified component. The target peaks were identified by standards toge-ther with databases of Dendrobium, Nature Chemistry, MassBank, etc. Finally, four active components, including 3,5,9-trihydroxy-23-methylergosta-7,22-dien-6-one, diacylglycerol(14∶1/22∶6/0∶0), pipercitine, and 22-tricosenoic acid, might have negative effect on the growth of gastric cancer cells.

Tenggerimyces flavus sp. nov., isolated from soil in a karst cave, and emended description of the genus Tenggerimyces.

A novel actinomycete, designated strain S6R2A4-9T, was isolated from a soil sample collected from a karst cave in Henan Province, China, and subjected to a polyphasic taxonomic study. This isolate grew optimally at 25-28 °C, pH 6.5-8.0 and in the absence of NaCl. The substrate mycelium of the isolate was well developed with irregular branches. Aerial mycelium fragmented into long, rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain S6R2A4-9T resided in the cluster of the genus Tenggerimyces within the family Nocardioidaceae and shared the highest 16S rRNA gene sequence similarity (98.98 %) with Tenggerimyces mesophilus I12A-02601T. The G+C content of the genomic DNA was 67.0 mol%. The strain contained glucose, ribose and xylose in its whole-cell hydrolysates. Strain S6R2A4-9T possessed a novel variation of peptidoglycan derived from the type A1γ meso-Dpm-direct. The polar lipids consisted of diphosphatidylglycerol, N-acetylglucosamine-containing phospholipid, phosphatidylinositol mannoside, phosphatidylglycerol, phosphoglycolipids and glycolipids. The predominant menaquinones were MK-10(H6) and MK-10(H8). The major fatty acids were C16 : 0, iso-C16 : 0 and 10-methyl C17 : 0. The level of DNA-DNA relatedness between strain S6R2A4-9T and T. mesophilus I12A-02601T was 27.6 ± 3.0 %, which was low enough to indicate that the strain represents a distinct species of the genus Tenggerimyces. On the basis of the polyphasic taxonomic evidence, a novel species, Tenggerimyces flavus sp. nov., is proposed. The type strain of the novel species is S6R2A4-9T ( = DSM 28944T = CGMCC 4.7241T).

Description of Salilacibacter albus gen. nov., sp. nov., isolated from a dried salt lake, and reclassification of Paraglycomyces xinjiangensis Luo et al. 2015 as a later heterotypic synonym of Salininema proteolyticum Nikou et al. 2015 with emended descriptions of the genus Salininema and Salininema proteolyticum.

A novel halophilic actinomycete, designated strain J11Y309T, was isolated from a soil sample collected from a dried salt lake in China. This isolate grew optimally at 28‒37 °C, with 3‒5 % (w/v) NaCl and at pH 7.0‒7.5. It contained meso-diaminopimelic acid as the diagnostic diamino acid and glucose, ribose and xylose were present in the whole-cell hydrolysates. MK-10(H4) was detected as the predominant menaquinone. The major fatty acids were anteiso-C17 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C15 : 0. Polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, phosphoglycolipids, glycolipids, an unidentified phospholipid and additional unidentified lipids. The G+C content of the genomic DNA was 63.0 mol%. The novel strain shared highest 16S rRNA gene sequence similarity with Salininema proteolyticum Miq-4T (95.80 %), Paraglycomyces xinjiangensis TRM 49201T (95.77 %) and Haloglycomyces albus YIM 92370T (94.84 %). Phylogenetic trees showed that it could not be clearly assigned to any known genus within the family Glycomycetaceae and formed a distinct phylogenetic line in the clade comprising members of the genera Salininema, Paraglycomyces and Haloglycomyces. Based on data from the present polyphasic taxonomic study, strain J11Y309T represents a novel species of a new genus in the family Glycomycetaceae, for which the name Salilacibacter albus gen. nov., sp. nov. is proposed with Salilacibacter albus sp. nov. as the type species. The type strain of Salilacibacter albus is J11Y309T (=DSM 46875T=CGMCC 4.7242T=LMG 29297T). Reclassification of Paraglycomyces xinjiangensis Luo et al. 2015 as a later heterotypic synonym of Salininema roteolyticum Nikou et al. 2015 is also discussed in this study.

Lysinibacter cavernae gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a karst cave.

A Gram-stain-positive, aerobic, straight or slightly bent rod-shaped, non-motile, non-spore-forming bacterium, designated strain CC5-806T, was isolated from a soil sample collected from a wild karst cave in the Wulong region, Chongqing, PR China and examined using a polyphasic approach to clarify its taxonomic position. This bacterium did not produce substrate mycelium or aerial hyphae, and no diffusible pigments were observed on the media tested. Strain CC5-806T grew optimally without NaCl at 20 °C and at pH 7.0. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain CC5-806T belonged to the family Microbacteriaceae and showed the highest levels of 16S rRNA gene sequence similarities with Frigoribacterium endophyticum EGI 6500707T (97.56 %), Frigoribacterium faeni 801T (97.53 %) and Glaciihabitans tibetensis MP203T (97.42 %). Phylogenetic trees revealed that strain CC5-806T did not show a clear affiliation to any genus within the family Microbacteriaceae. The DNA G+C content of strain CC5-806T was 62.6 mol%. The cell-wall peptidoglycan contained l-lysine as a diagnostic diamino acid. The predominant menaquinones were MK-11, MK-10 and MK-9. Phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid, four unidentified phospholipids and other polar lipids were detected in the polar lipid extracts. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. On the basis of the phylogenetic analysis, and phenotypic and chemotaxonomic characteristics, strain CC5-806T was distinguishable from phylogenetically related genera in the family Microbacteriaceae. It represents a novel species of a novel genus, for which the name Lysinibacter cavernae gen. nov., sp. nov. is proposed. The type strain is CC5-806T ( = DSM 27960T = CGMCC 1.14983T).

Nesterenkonia populi sp. nov., an actinobacterium isolated from Populus euphratica.

An alkaliphilic and moderately halophilic actinobacterium, designated strain GP10-3(T), was isolated from Populus euphratica collected from the southern edge of Taklimakan desert, Xinjiang, China. Cells of this strain were Gram-stain-positive, non-motile and non-spore-forming short rods. Strain GP10-3(T) grew optimally at 37 °C on LB agar media in the presence of 5-10% (w/v) NaCl at pH 9.0. The menaquinones were MK-7, MK-8 and MK-9. The major fatty acids (>10%) were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The peptidoglycan type was variation A4α, L-Lys-L-Glu. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylglycolipid, phosphatidylcholine, phosphatidylinositol, glycolipid and an unidentified phospholipid. The DNA G+C content was 67.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain GP10-3(T) belonged to the genus Nesterenkonia , sharing 94.6-96.9% sequence similarity with the type strains of species within this genus with validly published names. Based on the evidence of the polyphasic taxonomic study, strain GP10-3(T) represents a novel species of the genus Nesterenkonia , for which the name Nesterenkonia populi sp. nov. is proposed. The type strain is GP10-3(T) ( = DSM 27959(T) = KCTC 29119(T)).

Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil.

A rod- or coccus-shaped, non-spore-forming actinobacterium, designated strain SC8A-24(T), was isolated from a soil sample collected from the rhizosphere of Alhagi sparsifolia on the southern edge of the Taklimakan desert, Xinjiang, China, and examined by a polyphasic approach to clarify its taxonomic position. This actinobacterium was Gram-staining-positive and aerobic. Substrate and aerial mycelia were not observed, and no diffusible pigments were observed on the media tested. Strain SC8A-24(T) grew optimally without NaCl at 28-30 °C and pH 7.0-8.0. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain SC8A-24(T) belonged to the genus Nocardioides and shared the highest 16S rRNA gene sequence similarity with Nocardioides salarius CL-Z59(T) (96.51%), N. pyridinolyticus OS4(T) (96.43%) and N. ginsengagri BX5-10(T) (96.37%). The DNA G+C content of strain SC8A-24(T) was 71 mol%. The cell-wall peptidoglycan contained ll-2,6-diaminopimelic acid, and MK-8(H4) was the predominant menaquinone. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. The major fatty acids were C17 : 1ω8c, 10-methyl C17 : 0 and C18 : 1ω9c. On the basis of phylogenetic analysis and phenotypic and chemotaxonomic characteristics, strain SC8A-24(T) represents a novel species of the genus Nocardioides , for which the name Nocardioides deserti sp. nov. is proposed. The type strain is SC8A-24(T) ( =DSM 26045(T)  = CGMCC 4.7183(T)).

Prauserella endophytica sp. nov., an endophytic actinobacterium isolated from Tamarix taklamakanensis.

A novel endophytic actinobacterium, designated strain SP28S-3(T), was isolated from a surface-sterilized stem of Tamarix taklamakanensis collected from the southern edge of Taklamakan desert, Xinjiang, China. Strain SP28S-3(T) was found to show chemotaxonomic and morphological properties consistent with its classification in the genus Prauserella. The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphoglycolipid, phosphatidylcholine, phosphatidylinositol, a glycolipid, an aminolipid and unidentified phospholipids. The major fatty acids (>10 %) were identified as iso-C16:0 and C16:0. The genomic DNA G+C content was determined to be 69.7 mol%. Phylogenetic analysis of strain SP28S-3(T) clearly showed that the strain had the highest similarity of 16S rRNA gene sequence with Prauserella coralliicola SCSIO 11529(T) (99.9 %), followed by Prauserella marina DSM 45268(T) (97.0 %) and is affiliated with the genus Prauserella. The low level (47.8 ± 5.5 %) of DNA-DNA relatedness between strain SP28S-3(T) and P. coralliicola SCSIO 11529(T) combined with other polyphasic taxonomic evidence clearly support the conclusion that strain SP28S-3(T) represents a novel Prauserella species, for which the name Prauserella endophytica sp. nov. is proposed. The type strain is SP28S-3(T) (=DSM 46655(T) = CGMCC 4.7182 (T)).

Neuroprotective effects of dendrobium endophytes metabolites in SH-SY5Y cells via the Nrf2/Keap1 pathway.

Recent studies have revealed that endophytes in plants can produce metabolites with activity that is comparable to or identical to the host. Dendrobine has attracted much attention in the field of neurodegenerative diseases by exhibiting anti-oxidative stress and neuroprotective effects. This study aimed to investigate the protective effects and mechanisms of metabolites of dendrobium endophytes Pseudomonas protegens CM-YJ44 and Priestia megaterium D-HT207 against H2O2-induced oxidative stress injury in SH-SY5Y cells. Results showed that there were 50 neuroprotective compounds in CM-YJ44 and 72 neuroprotective compounds in D-HT207. Those both increased significantly cell viability, decreased contents of ROS in H2O2-induced SH-SY5Y cells. It was confirmed that metabolites of CM-YJ44 and D-HT207 inhibited the H2O2-induced oxidative stress injury in SH-SY5Y cells, which mechanism is related to inhibition of ROS production, alteration of MMP, and inhibition of apoptosis and inflammatory factors expression via the Nrf2/Keap1 pathway.

Antimicrobial activity and comparative metabolomic analysis of Priestia megaterium strains derived from potato and dendrobium.

The growth of endophytic bacteria is influenced by the host plants and their secondary metabolites and activities. In this study, P. megaterium P-NA14 and P. megaterium D-HT207 were isolated from potato tuber and dendrobium stem respectively. They were both identified as Priestia megaterium. The antimicrobial activities and metabolites of both strains were explored. For antimicrobial activities, results showed that P. megaterium P-NA14 exhibited a stronger inhibition effect on the pathogen of dendrobium, while P. megaterium D-HT207 exhibited a stronger inhibition effect on the pathogen of potato. The supernatant of P. megaterium P-NA14 showed an inhibition effect only on Staphylococcus aureus, while the sediment of P. megaterium D-HT207 showed an inhibition effect only on Escherichia coli. For metabolomic analysis, the content of L-phenylalanine in P. megaterium P-NA14 was higher than that of P. megaterium D-HT207, and several key downstream metabolites of L-phenylalanine were associated with inhibition of S. aureus including tyrosine, capsaicin, etc. Therefore, we speculated that the different antimicrobial activities between P. megaterium P-NA14 and P. megaterium D-HT207 were possibly related to the content of L-phenylalanine and its metabolites. This study preliminarily explored why the same strains isolated from different hosts exhibit different activities from the perspective of metabolomics.

Combined metabolomics and proteomics to reveal beneficial mechanisms of Dendrobium fimbriatum against gastric mucosal injury.

As a dietary and medicinal plant, Dendrobium fimbriatum (DF) is widely utilized in China for improving stomach disease for centuries. However, the underlying mechanisms against gastric mucosal injury have not been fully disclosed. Here, metabolomics and proteomics were integrated to clarify the in-depth molecular mechanisms using cyclophosphamide-induced gastric mucosal injury model in mice. As a result, three metabolic pathways, such as creatine metabolism, arginine and proline metabolism, and pyrimidine metabolism were hit contributing to DF protective benefits. Additionally, γ-L-glutamyl-putrescine, cytosine, and thymine might be the eligible biomarkers to reflect gastric mucosal injury tatus, and DF anti-gastric mucosal injury effects were mediated by the so-called target proteins such as Ckm, Arg1, Ctps2, Pycr3, and Cmpk2. This finding provided meaningful information for the molecular mechanisms of DF and also offered a promising strategy to clarify the therapeutic mechanisms of functional foods.

Analysis of Endophytic Bacterial Diversity From Different Dendrobium Stems and Discovery of an Endophyte Produced Dendrobine-Type Sesquiterpenoid Alkaloids.

As the unique component of Dendrobium, dendrobine-type sesquiterpenoid alkaloids (DSAs) possess a variety of medicinal properties. It has been well documented that plant endophytes can in vitro synthesize secondary metabolites identical or similar to metabolites produced by their host plants. This study aimed to investigate the composition and distribution of endophytic bacteria of Dendrobium stems by Illumina MiSeq platform sequencing and cultivation-dependent methods and then to assess the potential for endophytic bacteria to produce DSAs. Results indicated that it was necessary to combine both cultivation-dependent and cultivation-independent methods to analyze the community structure of endophytic bacterial in plants comprehensively. The length of the Dendrobium stems influenced the endophytic bacterial community. The diversity and richness of endophytic bacteria in group J10_15cm of stems were the highest, which showed a significant difference from the other stem groups. However, there was no certain connection between the diversity and richness of endophytic bacteria and the content of dendrobine. It was most likely due to the influence of several specific endophytic bacteria genera, such as Sphingomonas and Rhodococcus. Athelia rolfsii, Myrothecium roridum, as pathogenic fungi, and Pectobacterium carotovorum subsp. actinidiae, as pathogenic bacteria of Dendrobium, were used to determine the antimicrobial activities. In these assays, six strains belonging to five genera showed antimicrobial activity against at least two phytopathogens. The strain BL-YJ10_15-29 (Paracoccus pueri THG-N2.35, 98.98%) showed the best antimicrobial activity against the three phytopathogens. In addition, 2 DSAs (6-hydroxydendrobine and nobilonine) were identified in the fermentation supernatant of the strain CM-YJ10_15-44 (Pseudomonas protegens CHA0, 99.24%), whereas the whole-genome analysis results further demonstrated that the precursors of the two DSAs [geranyl-PP and (E, E)-famesyl-PP] were synthesized mainly through the methyl-D-erythritol 4-phosphate pathway in this strain. This study provides new insight into the studies on the biosynthesis of DSAs and provides potential biocontrol bacteria.

Antimicrobial Activity Against Phytopathogens and Inhibitory Activity on Solanine in Potatoes of the Endophytic Bacteria Isolated From Potato Tubers.

As an important global crop, the potato (Solanum tuberosum L.) contains the endotoxin solanine that leads to human poisoning and major economic losses. Poisoning symptoms and even acute poisoning may occur when the content of solanine in potatoes exceeds 200 mg/kg. In addition, potatoes are susceptible to some pathogenic bacteria, including Streptomyces scabies and Erwinia carotovora subsp. atroseptica (Van Hall) dye, which can cause potato scab and potato blackleg disease, respectively. In this study, 37 culturable endophytic bacteria strains were obtained from potato tubers based on the culture-dependent method. Results indicated that nine strains showed antimicrobial activity against at least one pathogen by antimicrobial activity screening and 23 strains showed inhibitory activity on solanine in potato tubers. Among them, strain P-NA2-14 (Bacillus megaterium NBRC 15308T, 99.31%) showed not only better antimicrobial activity against both the two indicator pathogens, but also the best inhibitory activity on solanine, which was proved to be a potential biocontrol bacterium. Meanwhile, the relationship between the distribution of the endophytic bacterial community and the content of solanine in potato tubers was studied by Illumina-based analysis, indicating that the distribution of the endophytic bacterial community was obviously influenced by the content of solanine. The results showed a new insight into the relationship between plant secondary metabolites and endophytic bacteria in potato tubers and provided potential new technical support for the biological control of potato storage.

Diversity of culture-independent bacteria and antimicrobial activity of culturable endophytic bacteria isolated from different Dendrobium stems.

Dendrobium is known for its pharmacological actions including anti-cancer effect, anti-fatigue effect, gastric ulcer protective effect, and so on. At present, only studies on endophytic fungi of Dendrobium affecting the metabolites of host plants have been reported, very little research has been done on endophytic bacteria. In this study, we have demonstrated the great diversity of endophytic bacteria in 6 Dendrobium samples from different origins and cultivars. According to the results of the culture-independent method, the endophytic bacterial community in Dendrobium stems showed obvious different in the 6 samples and was influenced by origin and cultivar. Some bacteria including Ralstonia, Comamonas and Lelliottia were first detected in Dendrobium in this study. Based on the culture-dependent method, a total of 165 cultivable endophytic bacteria isolates were isolated from the sterilized Dendrobium stems, and were classified into 43 species according to the 16S rRNA gene sequence analysis. Moreover, 14 of the 43 strains showed antimicrobial activity against phytopathogen using the Kirby-Bauer method. Strain NA-HTong-7 (Bacillus megaterium, 99.12%) showed the highest antimicrobial activity. This study was the first comprehensive study on endophytic bacteria of Dendrobium from different origins and cultivars, which provides new insights into the endophytic bacteria from Dendrobium.