Studying bona fide SARS-CoV-2 biology in a BSL-2 biosafety environment using a split-virus-genome system

<正>Dear Editor,Severe acute respiratory syndrome coronavirus 2(SARSCoV-2) was identified as the pathogen causing the coronavirus disease(COVID-19), which sometimes resulted in fatal pneumonia(Hu et al., 2021). SARS-CoV-2 is a biosafety level 3(BSL-3) pathogen, and the requirement for high containment conditions is a bottleneck for basic research on viral biology.     

Inevitability or contingency: how many chromosomes do we really need?

<正>In an essay written by the evolutionary biologist Theodosius Dobzhansky in 1973, he pointed out that "Nothing in Biology Makes Sense Except in the Light of Evolution." An interesting phenomenon in biology is the presence of variable numbers of chromosomes in different organisms. Besides several species, which possess multiple circular chromosomes or simply linear chromosomes (Baril et al.1989; Suwanto and Kaplan, 1989; Jumas-Bilak et al., 1998),most prokaryotes only possess one circular chromosome. In contrast, the genomes of eukaryotic species are usually packaged into linear chromosomes with numbers varying     

Sodium (±)‐5‐bromo‐2‐(α‐hydroxypentyl) benzoate ameliorates pressure overload‐induced cardiac hypertrophy and dysfunction through inhibiting autophagy

Sodium (±)‐5‐bromo‐2‐(a‐hydroxypentyl) benzoate (generic name: brozopine, BZP) has been reported to protect against stroke‐induced brain injury and was approved for Phase II clinical trials for treatment of stroke‐related brain damage by the China Food and Drug Administration (CFDA). However, the role of BZP in cardiac diseases, especially in pressure overload‐induced cardiac hypertrophy and heart failure, remains to be investigated. In the present study, angiotensin II stimulation and transverse aortic constriction were employed to induce cardiomyocyte hypertrophy in vitro and in vivo, respectively, prior to the assessment of myocardial cell autophagy. We observed that BZP administration ameliorated cardiomyocyte hypertrophy and excessive autophagic activity. Further results indicated that AMP‐activated protein kinase (AMPK)‐mediated activation of the mammalian target of rapamycin (mTOR) pathway likely played a role in regulation of autophagy by BZP after Ang II stimulation. The activation of AMPK with metformin reversed the BZP‐induced suppression of autophagy. Finally, for the first time, we demonstrated that BZP could protect the heart from pressure overload‐induced hypertrophy and dysfunction, and this effect is associated with its inhibition of maladaptive cardiomyocyte autophagy through the AMPK‐mTOR signalling pathway. These findings indicated that BZP may serve as a promising compound for treatment of pressure overload‐induced cardiac remodelling and heart failure.     

Analysis of autophagy genes in microalgae: chlorella as a potential model to study mechanism of autophagy

Background

Microalgae, with the ability to mitigate CO₂ emission and produce carbohydrates and lipids, are considered one of the most promising resources for producing bioenergy. Recently, we discovered that autophagy plays a critical role in the metabolism of photosynthetic system and lipids production. So far, more than 30-autophagy related (ATG) genes in all subtypes of autophagy have been identified. However, compared with yeast and mammals, in silico and experimental research of autophagy pathways in microalgae remained limited and fragmentary.

Principal Findings

In this article, we performed a genome-wide analysis of ATG genes in 7 microalgae species and explored their distributions, domain structures and evolution. Eighteen “core autophagy machinery” proteins, four mammalian-specific ATG proteins and more than 30 additional proteins (including “receptor-adaptor” complexes) in all subtypes of autophagy were analyzed. Data revealed that receptor proteins in cytoplasm-to-vacuole targeting and mitophagy seem to be absent in microalgae. However, most of the “core autophagy machinery” and mammalian-specific proteins are conserved among microalgae, except for the ATG9-cycling system in Chlamydomonas reinhardtii and the second ubiquitin-like protein conjugation complex in several algal species. The catalytic and binding residues in ATG3, ATG5, ATG7, ATG8, ATG10 and ATG12 are also conserved and the phylogenetic tree of ATG8 coincides well with the phylogenies. Chlorella contains the entire set of the core autophagy machinery. In addition, RT-PCR analysis verified that all crucial ATG genes tested are expressed during autophagy in both Chlorella and Chlamydomonas reinhardtii. Finally, we discovered that addition of 3-Methyladenine (a PI3K specific inhibitor) could suppress the formation of autophagic vacuoles in Chlorella.

Conclusions

Taken together, Chlorella may represent a potential model organism to investigate autophagy pathways in photosynthetic eukaryotes. The study will not only promote understanding of the general features of autophagic pathways, but also benefit the production of Chlorella-derived biofuel with future commercial applications.     

合成基因组学：设计与合成的艺术

随着基因组相关技术(测序、编辑、合成等)和知识(功能基因组学)的日益成熟,合成基因组学在本世纪迎得了发展的契机。病毒、原核生物的全基因组相继被化学合成并支持生命的存活,第1个真核生物合成基因组计划已经完成过半,人类基因组编写计划提上日程。在基因组合成的实践过程中,研究者们不断探索对基因组进行重编和设计所应遵循的规则,提高从头合成、组装和替换基因组的技术手段。合成基因组在工业、环境、健康和基础研究领域有着广阔的应用前景,同时也带来了相应的伦理问题。结合在Sc2.0计划中的基因组合成研究和近期合成基因组学所取得的重大进展,本文综述了基因组设计和合成相关的科学、技术和伦理内容,并探讨了未来发展所面对的挑战。作为合成生物学最重要的领域之一,合成基因组学方兴未艾。     

Characterization of an ammonium transporter in the oleaginous alga Chlorella protothecoides

A suppression subtractive hybridization cDNA library was used to screen the differently expressed (up-regulated) genes in the photosynthesis–fermentation approach (PFA) of Chlorella protothecoides cultivation. A total of 87 clones were obtained and sequenced, in which 78 clones were homologous to known genes in databases. Among them, the ammonium transporter gene (CpAMT1) was characterized in detail. Quantitative real-time PCR showed that the expression of CpAMT1 was significantly induced by PFA and correlated with lipid accumulation. The up-regulation of CpAMT1 was suppressed by glutamine, while the lipid biosynthesis was also inhibited. Further analysis showed that the expression of CpAMT1 was correlated with glutamine synthetase activity, suggesting that CpAMT1, along with glutamine synthetase/glutamate synthase, may be responsible for nitrogen sensing in C. protothecoides. Together, these results imply that the ammonium transporter CpAMT1 could be the initial sensor of nitrogen deficiency and channels the carbon excess toward lipid biosynthesis.     

Identification of Clausine E as an inhibitor of fat mass and obesity‐associated protein (FTO) demethylase activity

The alkaloids containing a carbazole nucleus are an established class of natural products with wide range of biological activities. A combination of thermodynamic and enzymatic activity studies provides an insight into the recognition of Clausine E by the fat mass and obesity‐associated protein (FTO). The binding of Clausine E to FTO was driven by positive entropy and negative enthalpy changes. Results also indicated that the hydroxyl group was crucial for the binding of small molecules with FTO. The structural and thermodynamic information provides the basis for the design of more effective inhibitors for FTO demethylase activity.