Machado Henrique, Sonnenschein Eva C, Melchiorsen Jette, Gram Lone
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allè 6, DK-2970, Hørsholm, Denmark.
Department of Systems Biology, Technical University of Denmark, Matematiktorvet bldg 301, DK-2800, Kgs Lyngby, Denmark.
BMC Genomics. 2015 Mar 7;16(1):158. doi: 10.1186/s12864-015-1365-z.
Antibiotic resistance in bacteria spreads quickly, overtaking the pace at which new compounds are discovered and this emphasizes the immediate need to discover new compounds for control of infectious diseases. Terrestrial bacteria have for decades been investigated as a source of bioactive compounds leading to successful applications in pharmaceutical and biotech industries. Marine bacteria have so far not been exploited to the same extent; however, they are believed to harbor a multitude of novel bioactive chemistry. To explore this potential, genomes of 21 marine Alpha- and Gammaproteobacteria collected during the Galathea 3 expedition were sequenced and mined for natural product encoding gene clusters.
Independently of genome size, bacteria of all tested genera carried a large number of clusters encoding different potential bioactivities, especially within the Vibrionaceae and Pseudoalteromonadaceae families. A very high potential was identified in pigmented pseudoalteromonads with up to 20 clusters in a single strain, mostly NRPSs and NRPS-PKS hybrids. Furthermore, regulatory elements in bioactivity-related pathways including chitin metabolism, quorum sensing and iron scavenging systems were investigated both in silico and in vitro. Genes with siderophore function were identified in 50% of the strains, however, all but one harboured the ferric-uptake-regulator gene. Genes encoding the syntethase of acylated homoserine lactones were found in Roseobacter-clade bacteria, but not in the Vibrionaceae strains and only in one Pseudoalteromonas strains. The understanding and manipulation of these elements can help in the discovery and production of new compounds never identified under regular laboratory cultivation conditions. High chitinolytic potential was demonstrated and verified for Vibrio and Pseudoalteromonas species that commonly live in close association with eukaryotic organisms in the environment. Chitin regulation by the ChiS histidine-kinase seems to be a general trait of the Vibrionaceae family, however it is absent in the Pseudomonadaceae. Hence, the degree to which chitin influences secondary metabolism in marine bacteria is not known.
Utilizing the rapidly developing sequencing technologies and software tools in combination with phenotypic in vitro assays, we demonstrated the high bioactive potential of marine bacteria in an efficient, straightforward manner - an approach that will facilitate natural product discovery in the future.
细菌中的抗生素耐药性迅速传播，超过了新化合物的发现速度，这凸显了立即发现用于控制传染病的新化合物的必要性。几十年来，陆地细菌一直作为生物活性化合物的来源进行研究，并在制药和生物技术产业中取得了成功应用。海洋细菌目前尚未得到同样程度的开发；然而，人们认为它们含有大量新型生物活性化学物质。为了探索这种潜力，对加拉泰亚3号探险期间收集的21种海洋α-和γ-变形菌的基因组进行了测序，并挖掘了天然产物编码基因簇。
无论基因组大小如何，所有测试属的细菌都携带大量编码不同潜在生物活性的基因簇，特别是在弧菌科和假交替单胞菌科中。在色素沉着的假交替单胞菌中发现了非常高的潜力，单个菌株中多达20个基因簇，主要是NRPS和NRPS-PKS杂交体。此外，还通过计算机模拟和体外实验研究了生物活性相关途径中的调控元件，包括几丁质代谢、群体感应和铁清除系统。在50%的菌株中鉴定出具有铁载体功能的基因，然而，除了一个菌株外，所有菌株都含有铁摄取调节基因。在玫瑰杆菌属细菌中发现了编码酰化高丝氨酸内酯合成酶的基因，但在弧菌科菌株中未发现，仅在一个假交替单胞菌菌株中发现。对这些元件的理解和操纵有助于发现和生产在常规实验室培养条件下从未鉴定出的新化合物。在环境中通常与真核生物密切相关的弧菌属和假交替单胞菌属物种中，证实并验证了高几丁质分解潜力。几丁质通过ChiS组氨酸激酶的调控似乎是弧菌科的一个普遍特征，然而在假单胞菌科中不存在。因此，几丁质对海洋细菌次生代谢的影响程度尚不清楚。
利用快速发展的测序技术和软件工具，结合体外表型分析，我们以高效、直接的方式证明了海洋细菌的高生物活性潜力——这种方法将有助于未来天然产物的发现。
