Synthetic biology and metabolic engineering of actinomycetes for natural product discovery

Actinomycetes are one of the most valuable sources of natural products with industrial and medicinal importance. After more than half a century of exploitation, it has become increasingly challenging to find novel natural products with useful properties as the same known compounds are often repeatedly re-discovered when using traditional approaches. Modern genome mining approaches have led to the discovery of new biosynthetic gene clusters, thus indicating that actinomycetes still harbor a huge unexploited potential to produce novel natural products. In recent years, innovative synthetic biology and metabolic engineering tools have greatly accelerated the discovery of new natural products and the engineering of actinomycetes. In the first part of this review, we outline the successful application of metabolic engineering to optimize natural product production, focusing on the use of multi-omics data, genome-scale metabolic models, rational approaches to balance precursor pools, and the engineering of regulatory genes and regulatory elements. In the second part, we summarize the recent advances of synthetic biology for actinomycetal metabolic engineering including cluster assembly, cloning and expression, CRISPR/Cas9 technologies, and chassis strain development for natural product overproduction and discovery. Finally, we describe new advances in reprogramming biosynthetic pathways through polyketide synthase and non-ribosomal peptide synthetase engineering. These new developments are expected to revitalize discovery and development of new natural products with medicinal and other industrial applications.     

Logistic模型预测东北越冬代水稻二化螟发生期

2001~2003年在吉林省柳河县绿色大米生产稻区,采用Logistic模型拟合越冬代二化螟Chilosuppressalis(Walker),有效积温和诱捕器诱蛾百分率的关系。结果表明logistic模型有较好的拟合性。由模型拟合结果预测当地越冬代二化螟发蛾始盛期、高峰期和盛末期所需有效积温分别为275.9,358.4和440.8日.度,可以适时指导大田防治。     

Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO.

Shotgun proteomics is rapidly becoming one of the most efficient and popular tools to examine protein expression in cells. Numerous laboratories now have a wide array of low- and high-performance mass spectrometry instrumentation necessary to complete proteome-wide projects. Often these laboratories have time and financial constraints that prohibit all projects from being conducted on high-performance state-of-the-art mass spectrometers. Here, we compare shotgun proteomic results using a direct 'lyse, digest and analyse' approach on a high-performance mass spectrometer (i.e. the LTQ-FT) with the results from a much lower-performance instrument (i.e. the LCQ-DUO) where, for the latter, various traditional protein pre-fractionation steps and gas-phase fractionation were used to increase the proteome coverage. Our results demonstrate that shotgun proteomic analyses conducted on the lower-performance LCQ-DUO mass spectrometer could adequately characterize a PhoP constitutive strain of Salmonella typhimurium if proteome pre-fractionation steps and gas-phase fractionation were included.     

几种氧代丙酸化合物在诱捕白纹伊蚊中的应用

为了从氧代丙酸化合物中筛选出对白纹伊蚊Aedes albopictus具有良好引诱效果的化合物,采用陷阱诱捕法分别测定了丙酮酸（α-氧代丙酸）、3-甲氧基-2-甲基-3-氧代丙酸、3-(苄氧基)-3-氧代丙酸和3-氨基-3-氧代丙酸4种氧代丙酸化合物及丙酸对白纹伊蚊成虫的诱捕效果。结果表明,在供试的5种化合物中,α-氧代丙酸、3-甲氧基-2-甲基-3-氧代丙酸和3-(苄氧基)-3-氧代丙酸3种氧代丙酸化合物及丙酸的诱捕效果显著,同剂量的各化合物对白纹伊蚊的诱蚊效果依次是3-甲氧基-2-甲基-3-氧代丙酸>3-(苄氧基)-3-氧代丙酸>α-氧代丙酸=丙酸。相同质量α-氧代丙酸∶3-(苄氧基)-3-氧代丙酸=1∶1至1∶2的配方比,具有协同增效作用,平均累计诱捕量均显著优于单组分α-氧代丙酸、3-(苄氧基)-3-氧代丙酸和对照纯水（P<0.05）。其中最优配方比是α-氧代丙酸∶3-(苄氧基)-3-氧代丙酸=1∶2,平均累计诱捕量比单组分α-氧代丙酸增加45.45%,比单组分3-(苄氧基)-3-氧代丙酸增加32.33%和比对照纯水增加73.11%（P<0.05）。现场诱蚊试验结果表明,根据相似相溶原理将液体的氧代丙酸（α-氧代丙酸、3-甲氧基-2-甲基-3-氧代丙酸）分别与固体的氧代丙酸（3-(苄氧基)-3-氧代丙酸）混配并结合陷阱诱捕器,能够显著提高对白纹伊蚊的持效性及诱捕数量（混合物60 d的累计诱蚊总数量是单组分的1.28~2.15倍）。研究结果为进一步开发适用于家居办公环境中使用的诱蚊剂提供了研究基础。     

信息素在文物害虫防治中的应用与展望

文物害虫会对文物古建筑造成不可逆的破坏,因此害虫防治是文物保护的重要工作。随着博物馆引入有害生物综合防治（Integrated Pest Management,IPM）策略,博物馆的害虫防治也开始遵循“预防为主,防治结合”理念。昆虫体外信息素是IPM中重要的技术手段。该技术可对害虫进行监测与诱杀,有利于对害虫发生规律的研究与数量控制。且信息素具有用量少,不接触文物等优点。本文概述信息素的发展、种类与功能,整理了文物害虫信息素及其应用中的遇到的问题,并展望信息素的应用前景。     

Trap‐shyness subsidence is a threshold function of mark–recapture interval in brown mudfish Neochanna apoda populations

The influence of capture interval on trap shyness, and temperature, rainfall and drought on capture probability (p) in 827 brown mudfish Neochanna apoda was quantified using mark–recapture models. In particular, it was hypothesized that the loss of trapping memory in marked N. apoda would lead to a capture‐interval threshold required to minimize trap shyness. Neochanna apoda trap shyness approximated a threshold response to capture interval, declining rapidly with increasing capture intervals up to 16·5 days, after which p remained constant. Tests for detecting trap‐dependent capture probability in Cormack–Jolly–Seber models failed to detect trap shyness in N. apoda capture histories with capture intervals averaging 16 days. This confirmed the applicability of the 16 day capture‐interval threshold for mark–recapture studies. Instead, N. apoda p was positively influenced by water temperature and rainfall during capture. These results imply that a threshold capture interval is required to minimize the trade‐off between the competing assumptions of population closure and p homogeneity between capture occasions in closed mark–recapture models. Moreover, environmental factors that influence behaviour could potentially confound abundance indices, and consequently abundance trends should be interpreted with caution in the face of long‐term climate change, such as with global warming.     

Testing the precision and sensitivity of density estimates obtained with a camera‐trap method revealed limitations and opportunities

The use of camera traps in ecology helps affordably address questions about the distribution and density of cryptic and mobile species. The random encounter model (REM) is a camera‐trap method that has been developed to estimate population densities using unmarked individuals. However, few studies have evaluated its reliability in the field, especially considering that this method relies on parameters obtained from collared animals (i.e., average speed, in km/h), which can be difficult to acquire at low cost and effort. Our objectives were to (1) assess the reliability of this camera‐trap method and (2) evaluate the influence of parameters coming from different populations on density estimates. We estimated a reference density of black bears (Ursus americanus) in Forillon National Park (Québec, Canada) using a spatial capture–recapture estimator based on hair‐snag stations. We calculated average speed using telemetry data acquired from four different bear populations located outside our study area and estimated densities using the REM. The reference density, determined with a Bayesian spatial capture–recapture model, was 2.87 individuals/10km² [95% CI: 2.41–3.45], which was slightly lower (although not significatively different) than the different densities estimated using REM (ranging from 4.06–5.38 bears/10km² depending on the average speed value used). Average speed values obtained from different populations had minor impacts on REM estimates when the difference in average speed between populations was low. Bias in speed values for slow‐moving species had more influence on REM density estimates than for fast‐moving species. We pointed out that a potential overestimation of density occurs when average speed is underestimated, that is, using GPS telemetry locations with large fix‐rate intervals. Our study suggests that REM could be an affordable alternative to conventional spatial capture–recapture, but highlights the need for further research to control for potential bias associated with speed values determined using GPS telemetry data.     

诱捕条件对红棕象甲聚集信息素田间效果的影响

红棕象甲Rhynchophorus ferrugineus Oliver是世界著名的严重危害棕榈植物的毁灭性入侵害虫,现已传入我国长江以南广大地区,对我国棕榈植物的安全生产造成严重威胁。本文比较了聚集信息素来源、诱捕器设置高度、颜色和类型对红棕象甲成虫诱捕效果的影响。结果表明:2种不同来源的红棕象甲聚集信息素诱捕效果无显著差异;诱捕器置于地面诱捕效果最好;红色和黑色诱捕器的诱虫量显著优于白色和黄色诱捕器;诱捕器类型对诱虫量无显著影响。本研究结果可为红棕象甲聚集信息素的监测技术提供指导。