Biochemical diversification through foreign gene expression in bdelloid rotifers.
Biochemical diversification through foreign gene expression in bdelloid rotifers.
复制标题
通过外源基因表达在嗜血杆菌旋转膜中的外源基因表达。
DOI：
10.1371/journal.pgen.1003035
复制
发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Tunnacliffe A
中科院分区：
文献类型：
--
作者：
Boschetti C;Carr A;Crisp A;Eyres I;Wang-Koh Y;Lubzens E;Barraclough TG;Micklem G;Tunnacliffe A
蛭形轮虫是一种具有独特特征的微型无脊椎动物：它们在没有有性繁殖的情况下存活了数千万年；它们通过脱水来抵御极端干燥；它们能忍受非常高水平的电离辐射。最近的证据表明，蛭形基因组的亚端粒区域包含通过水平基因转移（HGT）来自其他生物体的序列，其中一些已知是转录的。然而，外源基因表达在蛭体生理学中的作用程度尚不清楚。我们解决这个问题的第一个大型的转录组分析蛭形Adineta ricciae:蛭形轮虫受到水分和干燥的互补脱氧核糖核酸数据库大规模并行测序和组装记录相比对通过blastx UniProtKB数据库来识别他们的产品。在约29,000个匹配转录本中，约10%的转录本推断为水平获得，主要来自真细菌，也来自真菌、原生生物和藻类。在考虑到可能的误差来源后，HGT的比率至少为8%-9%，明显高于其他无脊椎动物。我们通过系统发育分析验证了它们的外源性，并证明了外源基因与蛭形基因组中后生动物基因的联系。在蛭形体中表达的水平获得基因中，约有80%编码酶，这些基因在已确定的途径中占39%的酶。与其他后生动物相比，由外源基因编码的许多酶可以增强蛭形生物的生物化学，例如，通过增强毒素降解或产生抗氧化剂和关键代谢物。它们还补充，有时可能取代现有的后生动物功能。因此蛭形轮虫以动物中前所未有的规模表达水平获得性基因，外源基因对它们的代谢有深远的贡献。这代表了古代无性动物快速适应变化环境的潜在机制，从而在没有性别的情况下持续了很长时间的进化。蛭形轮虫是一种微小的无脊椎动物，具有不同寻常的特征：它们能承受压力，如干燥和高水平的电离辐射，这些会杀死其他动物，它们在没有有性繁殖的情况下存活了数百万年，这与有性进化优势的理论相矛盾。在这项研究中，我们研究了蛭形虫的另一个奇怪的特征，即它们能够从其他生物体中获得基因，这一过程被称为水平基因转移（HGT）。我们发现HGT在蛭形体中以前所未有的规模发生：大约10%的活性基因是“外来的”，主要来自细菌和其他简单的生物，如真菌和藻类，但现在作为蛭形基因起作用。大约80%的外源基因编码酶，这些基因对蛭形生物化学做出了重大贡献；39%的酶活性有外源基因的贡献，在23%的情况下，所讨论的活性是由外源基因唯一指定的。这表明生物化学，如毒素降解和抗氧化剂的产生，在其他动物中是未知的，有望提高蛭体的“健壮性”。它还代表了一种可能的无性生存机制，通过功能能力的多样化，甚至用外来基因替代有缺陷的基因。
Bdelloid rotifers are microinvertebrates with unique characteristics: they have survived tens of millions of years without sexual reproduction; they withstand extreme desiccation by undergoing anhydrobiosis; and they tolerate very high levels of ionizing radiation. Recent evidence suggests that subtelomeric regions of the bdelloid genome contain sequences originating from other organisms by horizontal gene transfer (HGT), of which some are known to be transcribed. However, the extent to which foreign gene expression plays a role in bdelloid physiology is unknown. We address this in the first large scale analysis of the transcriptome of the bdelloid Adineta ricciae: cDNA libraries from hydrated and desiccated bdelloids were subjected to massively parallel sequencing and assembled transcripts compared against the UniProtKB database by blastx to identify their putative products. Of ∼29,000 matched transcripts, ∼10% were inferred from blastx matches to be horizontally acquired, mainly from eubacteria but also from fungi, protists, and algae. After allowing for possible sources of error, the rate of HGT is at least 8%–9%, a level significantly higher than other invertebrates. We verified their foreign nature by phylogenetic analysis and by demonstrating linkage of foreign genes with metazoan genes in the bdelloid genome. Approximately 80% of horizontally acquired genes expressed in bdelloids code for enzymes, and these represent 39% of enzymes in identified pathways. Many enzymes encoded by foreign genes enhance biochemistry in bdelloids compared to other metazoans, for example, by potentiating toxin degradation or generation of antioxidants and key metabolites. They also supplement, and occasionally potentially replace, existing metazoan functions. Bdelloid rotifers therefore express horizontally acquired genes on a scale unprecedented in animals, and foreign genes make a profound contribution to their metabolism. This represents a potential mechanism for ancient asexuals to adapt rapidly to changing environments and thereby persist over long evolutionary time periods in the absence of sex. Bdelloid rotifers are tiny invertebrates with unusual characteristics: they withstand stresses, such as desiccation and high levels of ionising radiation, that kill other animals, and they have survived over millions of years without sexual reproduction, which contradicts theories on the evolutionary advantages of sex. In this study, we investigate another bizarre feature of bdelloids, namely their ability to acquire genes from other organisms in a process known as horizontal gene transfer (HGT). We show that HGT happens on an unprecedented scale in bdelloids: approximately 10% of active genes are “foreign,” mostly originating from bacteria and other simple organisms like fungi and algae, but now functioning as bdelloid genes. About 80% of foreign genes code for enzymes, and these make a major contribution to bdelloid biochemistry: 39% of enzyme activities have a foreign contribution, and in 23% of cases the activity in question is uniquely specified by a foreign gene. This indicates biochemistry, such as toxin degradation and antioxidant generation, that is unknown in other animals and that is expected to improve the “robustness” of the bdelloid. It also represents a possible mechanism for survival without sex, by diversification of functional capacity and even replacement of defective genes by foreign counterparts.
登录
查看更多内容
DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
DOI：
10.1073/pnas.0712248105
发表时间：
2008-03-04
影响因子：
11.1
作者：
Martens, Cindy;Vandepoele, Klaas;Van de Peer, Yves
通讯作者：
Van de Peer, Yves
影响因子：
2.6
作者：
Kranner, I;Birtic, S
通讯作者：
Birtic, S
DOI：
10.1016/j.cbpb.2004.10.019
发表时间：
2004-12-01
影响因子：
2.3
作者：
Caprioli, M;Katholm, AK;Santo, N
通讯作者：
Santo, N
影响因子：
56.9
作者：
Hotopp, Julie C. Dunning;Clark, Michael E.;Werren, John H.
通讯作者：
Werren, John H.