Unleashing the potential: type I CRISPR-Cas systems in actinomycetes for genome editing.

Covering: up to the end of 2023Type I CRISPR-Cas systems are widely distributed, found in over 40% of bacteria and 80% of archaea. Among genome-sequenced actinomycetes (particularly Streptomyces spp.), 45.54% possess type I CRISPR-Cas systems. In comparison to widely used CRISPR systems like Cas9 or Cas12a, these endogenous CRISPR-Cas systems have significant advantages, including better compatibility, wide distribution, and ease of operation (since no exogenous Cas gene delivery is needed). Furthermore, type I CRISPR-Cas systems can simultaneously edit and regulate genes by adjusting the crRNA spacer length. Meanwhile, most actinomycetes are recalcitrant to genetic manipulation, hindering the discovery and engineering of natural products (NPs). The endogenous type I CRISPR-Cas systems in actinomycetes may offer a promising alternative to overcome these barriers. This review summarizes the challenges and recent advances in CRISPR-based genome engineering technologies for actinomycetes. It also presents and discusses how to establish and develop genome editing tools based on type I CRISPR-Cas systems in actinomycetes, with the aim of their future application in gene editing and the discovery of NPs in actinomycetes.

Dexmedetomidine alleviates cognitive impairment by promoting hippocampal neurogenesis via BDNF/TrkB/CREB signaling pathway in hypoxic-ischemic neonatal rats.

AIMS: Dexmedetomidine (DEX) has been reported to alleviate hypoxic-ischemic brain damage (HIBD) in neonates. This study aimed to investigate whether DEX improves cognitive impairment by promoting hippocampal neurogenesis via the BDNF/TrkB/CREB signaling pathway in neonatal rats with HIBD. METHODS: HIBD was induced in postnatal day 7 rats using the Rice-Vannucci method, and DEX (25 µg/kg) was administered intraperitoneally immediately after the HIBD induction. The BDNF/TrkB/CREB pathway was regulated by administering the TrkB receptor antagonist ANA-12 through intraperitoneal injection or by delivering adeno-associated virus (AAV)-shRNA-BDNF via intrahippocampal injection. Western blot was performed to measure the levels of BDNF, TrkB, and CREB. Immunofluorescence staining was utilized to identify the polarization of astrocytes and evaluate the levels of neurogenesis in the dentate gyrus of the hippocampus. Nissl and TTC staining were performed to evaluate the extent of neuronal damage. The MWM test was conducted to evaluate spatial learning and memory ability. RESULTS: The levels of BDNF and neurogenesis exhibited a notable decrease in the hippocampus of neonatal rats after HIBD, as determined by RNA-sequencing technology. Our results demonstrated that treatment with DEX effectively increased the protein expression of BDNF and the phosphorylation of TrkB and CREB, promoting neurogenesis in the dentate gyrus of the hippocampus in neonatal rats with HIBD. Specifically, DEX treatment significantly augmented the expression of BDNF in hippocampal astrocytes, while decreasing the proportion of detrimental A1 astrocytes and increasing the proportion of beneficial A2 astrocytes in neonatal rats with HIBD. Furthermore, inhibiting the BDNF/TrkB/CREB pathway using either ANA-12 or AAV-shRNA-BDNF significantly counteracted the advantageous outcomes of DEX on hippocampal neurogenesis, neuronal survival, and cognitive improvement. CONCLUSIONS: DEX promoted neurogenesis in the hippocampus by activating the BDNF/TrkB/CREB pathway through the induction of polarization of A1 astrocytes toward A2 astrocytes, subsequently mitigating neuronal damage and cognitive impairment in neonates with HIBD.

Polysaccharide from Ziyang Selenium-Enriched Green Tea Prevents Obesity and Promotes Adipose Thermogenesis via Modulating the Gut Microbiota.

The objective of the current study was to explore the potential mechanism of Ziyang selenium-enriched green tea polysaccharide (Se-GTP) against obesity. The results showed that Se-GTP significantly alleviated obesity and related metabolic disorders caused by high-fat diet (HFD) in mice. 16S rRNA gene sequencing results revealed that Se-GTP improved gut microbiota disturbance of obese mice and facilitated proliferation of probiotics such as Bacteroides, Bifidobacterium, Lactobacillus, and Akkermansia. In addition, the colonic content of succinate, a product of microbial metabolite in connection with adipocyte thermogenesis, was significantly enhanced by Se-GTP treatment. Therefore, Se-GTP facilitated brown adipose tissue (BAT) thermogenesis and inguinal white adipose tissue (iWAT) browning in obese mice, which could be revealed by increased expressions of thermogenic marker proteins UCP1, PGC-1α, and CIDEA in BAT and iWAT. Interestingly, Se-GTP intervention also observably increased the content of M2-like macrophages in iWAT of obese mice. To summarize, the results of this study are the first to show that Se-GTP can stimulate the browning of iWAT and BAT thermogenesis to counteract obesity, which may be pertinent with the alteration of gut microbiota in obese mice.

An in vitro CRISPR-Cas12a-mediated protocol for direct cloning of large DNA fragments.

Large biosynthetic gene cluster (BGC) cloning is important for discovering natural product-based drugs and remains challenging in high GC content microorganisms (e.g., Actinobacteria). Here, we present an in vitro CRISPR-Cas12a-mediated protocol for direct cloning of large DNA fragments. We describe steps for crRNA design and preparation, genomic DNA isolation, and CRISPR-Cas12a cleavage and capture plasmid construction and linearization. We then detail target BGC and plasmid DNA ligation and transformation and screening for positive clones. For complete details on the use and execution of this protocol, please refer to Liang et al.1.

Artemisia sphaerocephala Krasch polysaccharide promotes adipose thermogenesis and decreases obesity by shaping the gut microbiota.

This study was designed to investigate the underlying mechanism of Artemisia sphaerocephala Krasch polysaccharide (ASKP) against obesity. Here, our results showed that ASKP considerably reduced body weight gain and metabolic disorders in high fat diet (HFD)-fed mice. 16S rRNA gene sequencing revealed that ASKP relieved the gut microbiota disorder caused by HFD and promoted the proliferation of probiotics such as Lactobacillus, Bifidobacterium and Blautia. Interestingly, the fecal levels of succinate, a microbial metabolite associated with adipose thermogenesis, were dramatically elevated by ASKP treatment in obese mice. Accordingly, ASKP promoted thermogenesis of brown adipose tissue (BAT) and browning of inguinal white adipose tissue (iWAT) of mice fed with a HFD, as revealed by the elevated expression of thermogenic marker genes (UCP1, CIDEA and PGC1α) in BAT and iWAT. Importantly, antibiotic treatment significantly decreased the ASKP-elevated fecal levels of succinate and further abolished the adipose thermogenesis effects of ASKP. Taken together, our results show that ASKP prevents obesity through iWAT browning and BAT activation, a mechanism that is dependent on the gut microbiota metabolism.

Activating cryptic biosynthetic gene cluster through a CRISPR-Cas12a-mediated direct cloning approach.

Direct cloning of biosynthetic gene clusters (BGCs) from microbial genomes facilitates natural product-based drug discovery. Here, by combining Cas12a and the advanced features of bacterial artificial chromosome library construction, we developed a fast yet efficient in vitro platform for directly capturing large BGCs, named CAT-FISHING (CRISPR/Cas12a-mediated fast direct biosynthetic gene cluster cloning). As demonstrations, several large BGCs from different actinomycetal genomic DNA samples were efficiently captured by CAT-FISHING, the largest of which was 145 kb with 75% GC content. Furthermore, the directly cloned, 110 kb long, cryptic polyketide encoding BGC from Micromonospora sp. 181 was then heterologously expressed in a Streptomyces chassis. It turned out to be a new macrolactam compound, marinolactam A, which showed promising anticancer activity. Our results indicate that CAT-FISHING is a powerful method for complicated BGC cloning, and we believe that it would be an important asset to the entire community of natural product-based drug discovery.

False decrease of HBsAg S/CO values in serum with high-concentration rheumatoid factors.

OBJECTIVES: To investigate whether high-concentration RFs cause false decrease of S/CO values of serum HBsAg. DESIGN AND METHODS: Serum HBsAg was determined in 100 RF-positive sera using one-step ELISA. Twenty-three HBsAg-negative sera with high-concentration RFs were selected randomly to perform dilution with mixed normal sera. Serum models consisting of HBsAg and high-concentration RFs were made by blending high-concentration RFs and HBsAg-positive sera at the ratio of 9:1. RESULTS: In the 23 samples, one-step ELISA showed that HBsAg-positive rate was 69.57% at dilution of 1:2, 60.87% at dilution of 1:4 and 40.00% at dilution of 1:8, whereas two-step ELISA showed that it was 100% without any dilution. Thirty serum models were made and divided into six groups. Median S/CO value of HBsAg was 3.00 in control, whereas it ranged from 0.13 to 1.78 in the six groups. CONCLUSIONS: High-concentration RFs cause false decrease of S/CO values of HBsAg using one-step ELISA.

Rapid and reliable genotyping of HLA-B*27 in the Chinese Han population using a duplex real-time TaqMan PCR assay.

OBJECTIVES: To develop a duplex real-time TaqMan PCR assay for genotyping HLA-B*27 in the Chinese Han population. DESIGN AND METHODS: A standard curve was constituted to deduce amplification efficiency, dynamic range and detection limit of the duplex real-time TaqMan PCR assay, whereas PCR-SBT (PCR with sequence-based typing) was used to evaluate the accuracy of the assay. RESULTS: A linear standard curve for determining HLA-B*27 was obtained within the range of 10(1)-10(9) copies per reaction with the correlation coefficient of 0.99 and amplification efficiency of 98.30%. The detection limit was 3.09 copies per reaction. Complete concordance was found between the results obtained by the duplex real-time TaqMan PCR assay and PCR-SBT. Fifty-nine of the 178 genomic samples were HLA-B*27 positive and the other 119 were HLA-B*27 negative. CONCLUSIONS: The duplex real-time TaqMan PCR approach appears to be a reliable, sensitive, rapid and high-throughput method to genotype HLA-B*27 in the Chinese Han population.