喀译 | “为环境而生”和“因环境而生”的生物工具

本文译自cell.com

内附原文，转载请注明出处

有这样一种观点，期刊《生物技术趋势》（TIBTECH）的最终适用范围和受众群体应该是应用生物学。这种观点足以将TIBTECH与那些涵盖机械生物学或现象生物学的同类期刊区别开来。这当然是一个很好的出发点，意味着该期刊的有效性已被证明。但此类观点仍然有些过于宽泛了。

At its highest level, the scope and audience of Trends in Biotechnology (TIBTECH) is applied biology. That description suffices to distinguish TIBTECH from some of the other Trends journals, which cover more mechanistic or phenomenological biology. It is a good starting point; it implies demonstrated usefulness. But it is still staggeringly broad.

所谓“生物技术应用”，是否意味着利用来自生物学领域的工具、方法或化学个体，来解决非生物问题呢？就好比利用细胞代谢工程的方法来工业化生产化学制品；或者说，我们是否应该认为，“生物技术应用”是将在某些方面有价值的非生物技术转化到生物或医学领域中去？比如3D打印技术常被用来制作生物组织。当然，如果将某种生物学过程从它原始的环境里转移到另一个生物项目中并使其成功表现，比如将CRISPR/Cas系统从原核免疫领域应用到基因编辑领域，我们把这种过程叫做“生物技术应用”看来也十分合适。

Does applied, for instance, mean tools, methods, and chemical entities derived from biology used to solve nonbiological problems, like performing metabolic engineering on microbes to produce industrially useful chemicals? [1] Or, should we consider applied to refer to inorganic technology that has found some use being transferred to biological or medical contexts, such as 3D printing technology used to fabricate tissues? [2] Certainly, translating a biological process from its native context to perform another biological task, such as appropriating the CRISPR/Cas systems from prokaryote immunity to edit genomes across the domains of life, would seem to qualify as applied biology [3].

TIBTECH的专题特刊包含了许多基于不同定义的生物技术应用案例，各自都有在自然环境中应用的背景。有关“生物技术在自然环境中的应用”的相关话题经常特别吸引人，大家都尝试着更好地去解读应用生物学的本质，因为这能证明在多种不同情况下，小分子、基因、蛋白质、以及有机体都在自然环境中发挥了有效作用。

This special issue of TIBTECH covers applications in many different senses of the word; each in the context of environmental biotechnology. The topic of environmental biotechnology is particularly intriguing from the perspective of trying to better grasp the nature of applied biology because it demonstrates the usefulness of the small molecules, genes, proteins, and organisms present in the environment in so many different novel contexts.

其中有些情况是被用来解决环境问题，主要集中在“降解”和“修复”两大主题上。有四篇综述特别详述了微生物（及其相关酶）在去除油、水等液体中的污染物领域的应用：Chen介绍了纳米结构碳的生物降解作用；Tripathi及同事讨论了使用细菌群落及植物伴生微生物群来恢复土壤活性以求可持续发展；Gao解释了鞘脂单胞菌特别适合土壤修复的原因； Mapelli 及同事们阐述了微生物群是怎样分解泄漏至海洋的石油。

Some of these contexts are themselves solving environmental problems – largely centered on the theme of degradation and remediation. Four reviews specifically detail approaches to using microbes (and their associated enzymes) to remove pollutants from soil, water, and other environmental reservoirs: Chen et al. review biodegradation of nanostructured carbon; Tripathi and colleagues discuss using microbial consortia and plant-associated microorganisms to restore degraded land for sustainable development; Gao et al. explain why one particular class of microbes, the sphingomonads, might be especially well suited to remediating soil; and Mapelli and colleagues write about how microbes have been applied to clean up marine oil spills.

此外，有两篇小短文也介绍了微生物群是怎样在工业化生产中发挥了重要作用：Wang及同事推测，某种特定细菌所具备的无氧甲烷氧化脱氮能力可能更加有益于可持续的水体净化过程，Ghosh和Kiran提出了使用一种源自藻类的碳浓缩机制来降低废气中二氧化碳含量的理论。

In addition, two short articles discuss how microorganisms might play important roles in industrial processes: Wang and colleagues hypothesize that the denitrifying anaerobic methane oxidation capabilities of certain bacteria could be used for more sustainable wastewater treatment, and Ghosh and Kiran propose a process for using carbon-concentrating mechanisms native to algae to reduce carbon dioxide emissions from exhaust gas.

另一方面，源于环境中的生物学也可以作为一项技术，应用在农业、药理学、工业甚至是法医领域。Zhang及同事们回顾了通过干扰真核生物调节系统的RNA来提高农作物耐虫性的方法；一篇由Marmeisse及同事在其所作的综述中介绍了一些勘探真核生物基因的方法，并回答了这些基因是怎样被用来开辟创新合成生物学捷径的问题； Metcalf 及同事针对微生物群如何作为痕量证据在刑事审判系统中发挥作用提出了自己的看法。最后，由Parra、Quave及Singh所著短文探讨了如何分别利用本地知识和地衣内生菌为药类化合物提供新来源。

The other side of the coin is taking biology present in the environment and applying it as technology to agriculture, pharmacology, industry, and even forensics. Zhang and colleagues review using the eukaryotic regulatory system RNAi as an insect resistance strategy in crop plants; a review by Marmeisse and colleagues describes new methods for bioprospecting for eukaryotic genes and how these genes might be used to construct new synthetic biology pathways; and Metcalf and colleagues give their opinion on how the microbiome might find its way into the criminal justice system as trace evidence. Finally, short articles by de la Parra and Quave, and Singh and colleagues, discuss how to use indigenous knowledge and endolichenic fungi, respectively, as new sources for pharmaceutical compounds.

让生物学既能作为一种工具来解决环境问题，又把它从环境中提炼出来并赋予了新的任务，当然是不可能包含所有方面的。但是，我希望你们能够认可这样一种观点，即两种方法都在以它们自己的方式让生物学得以应用（也无疑包括生物技术）。

Of course, it is impossible to cover all of the many ways in which biology can either be used as a tool to address environmental problems or be discovered from the environment and repurposed. But, I hope you will agree that both are applied biology in their own way – and indubitably biotechnology.

参考文献：

[1] Wu，G.等，代谢的负担：合成生物学及代谢工程的应用基础 生物技术趋势 2016；34:652-664

Metabolic burden: cornerstones in synthetic biology and metabolic engineering applications.

[2] Gao，B.等，应用在生物医学的4D生物打印技术 生物技术趋势2016；34:746-756

4D bioprinting for biomedical applications.

[3] Mougiakos, I.等，下一代原核生物工程学： CRISPR-Cas工具 生物技术趋势  2016;34: 575–587

Next generation prokaryotic engineering: the CRISPR-Cas toolkit.