SANDPIT : Knots and Evolution - Topologically Driven Integrase Mutagenesis

SADPIT：结和进化 - 拓扑驱动的整合酶诱变

• 批准号: EP/H031367/1
• 负责人: Dorothy Buck
• 金额: $ 56.03万
• 依托单位: Imperial College London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2010
• 资助国家: 英国
• 起止时间: 2010 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FH031367%2F1
• 关键词: SANDPIT; Knots; Evolution; Topologically; Driven

Since their discovery in the late 1960s, DNA knots and links have been found to play key roles in hosts of cellular processes. Because they are so ubiquitous all organisms have developed special proteins whose function is to help untie DNA knots and links. There are also other important proteins-- called recombinases -- that can alter the order of the sequence of the DNA basepairs. While the main function of recombinases is to rearrange the order of basepairs, in the process of doing this they often cause changes to DNA knotting or linking. For all these reasons molecular biologists became interested in learning about knots and links. Mathematicians have studied knots since the late 19th century for their own reasons, having nothing to do with DNA. Mathematically a knot is a one-dimensional object sitting inside 3-space, just like a standard circle does, but which we cannot smoothly deform to a standard circle. The mathematical theory of knots and links turns out to be very rich and surprisingly complicated, and intimately related to general 3-dimensional spaces, called 3-manifolds. (The study of these spaces is called 3-manifold topology.) Although the subject is very deep, some of the simplest questions remain unanswered: even today if you hand the world's top knot theorists two sufficiently complicated knots there is no known algorithm they can use to always tell whether one knot can be deformed into the other. Using tools from knot theory, mathematicians have been able to help biologists better understand the ways some proteins interact with DNA. For example, mathematicians have developed models of how the recombinase proteins reshuffle the DNA sequence. (1) These models can then predict various new features of these interactions - e.g. particular geometric configuration the DNA takes when the protein is attached or what biochemical pathway the reactions proceeds through. Site-specific recombinases mediate the reshuffling of the DNA sequence is important because of its key role in a wide variety of biological processes and is an important mechanism for bacterial evolution e.g. the recent emergence of multiple antibiotic resistance mediated by integrons. The integron integrases are unusual in that they undertake a wide variety of recombination reactions and it is anticipated that there will be a wide variety of topologically distinct products generated. The form of the knotted products will be indicative of the type and frequency of recombination reactions that have occurred. A number of phylogenetically and evolutionary distinct integrases will be mechanistically studied and the topology of their products determined in order to gain insight into integrase evolution, the fundamental mechanisms of integron driven genome plasticity and bacterial evolution. DNA can form very complicated knots. But only a small fraction of all possible very complicated knots appear as DNA knots. One issue has been (2) determining which knots can show up after a recombinase acts on an initial family of DNA knot configurations. In this proposal we will explore these two arenas (1) and (2) for a large and important family of proteins, the integrases. To answer these questions, we will use cutting-edge techniques from 3-manifold topology, combined with novel microbiological experiments. The answers will help us understand these important evolutionary agents more completely.

自1960年代后期发现它们以来，DNA结和链接已被发现在蜂窝过程的宿主中起关键作用。因为它们无处不在，所有生物都开发了特殊的蛋白质，其功能是帮助解开DNA结和链接。还有其他重要的蛋白质（称为重物组织酶）可以改变DNA碱基序列的顺序。重点组酶的主要功能是重新排列底底，但在这样做的过程中，它们通常会导致DNA打结或链接的变化。由于所有这些原因，分子生物学家对学习结和链接感兴趣。自19世纪后期以来，数学家出于自己的原因就开始了结，与DNA无关。从数学上讲，一个结是一个坐在3空间内部的一维对象，就像标准圆一样，但是我们无法将其平滑地变形到标准圆。结和链接的数学理论证明非常丰富且令人惊讶地复杂，并且与一般的三维空间密切相关，称为3个manifolds。 （对这些空间的研究称为3型拓扑。）尽管该主题非常深入，但一些最简单的问题仍然没有得到解答：即使在今天，如果您将世界顶级结理论家递给两个足够复杂的结两个，那么他们都无法使用一个已知的算法来始终告诉一个结的算法。使用结理论的工具，数学家已经能够帮助生物学家更好地了解某些蛋白质与DNA相互作用的方式。例如，数学家已经开发了重组酶蛋白如何改组DNA序列的模型。 （1）然后这些模型可以预测这些相互作用的各种新特征，例如当蛋白质附着或反应通过的生化途径时，DNA采取的特定几何构型会采用。位点特异性重组酶介导DNA序列的改组非常重要，因为它在各种生物学过程中的关键作用，并且是细菌进化的重要机制，例如近期通过整合元介导的多种抗生素耐药性的出现。积分集成酶是不寻常的，因为它们进行了多种重组反应，并且预计会产生各种各样的拓扑上不同的产品。打结的产品的形式将指示发生的重组反应的类型和频率。将对许多系统发育和进化不同的积分进行机械研究，并确定其产品的拓扑结构，以便深入了解整合酶进化，Integron驱动的基因组可塑性和细菌进化的基本机制。 DNA会形成非常复杂的结。但是，只有一小部分可能非常复杂的结出是DNA结。一个问题是（2）确定重组酶在初始的DNA结构族的家族上作用后可以显示哪些结。在此提案中，我们将探索这两个领域（1）和（2），以获取大型而重要的蛋白质家族，即综合酶。为了回答这些问题，我们将使用来自3个Manifold拓扑的尖端技术，并结合新型的微生物实验。答案将帮助我们更完全了解这些重要的进化剂。

项目成果

Topological aspects of DNA function and protein folding.

DNA 功能和蛋白质折叠的拓扑方面。

• DOI: 10.1042/bst20130006
• 发表时间: 2013
• 期刊: Biochemical Society transactions
• 影响因子: 3.9
• 作者: Stasiak A

Topology and Geometry of Biopolymers

生物聚合物的拓扑和几何结构

• DOI: 10.1090/conm/746/15003
• 发表时间: 2020
• 作者: Buck D

Coherent band pathways between knots and links

• DOI: 10.1142/s0218216515500066
• 发表时间: 2015-02-01
• 期刊: JOURNAL OF KNOT THEORY AND ITS RAMIFICATIONS
• 影响因子: 0.5
• 作者: Buck, Dorothy;Ishihara, Kai
• 通讯作者: Ishihara, Kai

Rational tangle surgery and Xer recombination on catenanes

• DOI: 10.2140/agt.2012.12.1183
• 发表时间: 2012-01-01
• 期刊: ALGEBRAIC AND GEOMETRIC TOPOLOGY
• 影响因子: 0.7
• 作者: Darcy, Isabel K.;Ishihara, Kai;Shimokawa, Koya
• 通讯作者: Shimokawa, Koya

The classification of rational subtangle replacements between rational tangles

理性缠结之间理性子缠结替换的分类

• DOI: 10.2140/agt.2013.13.1413
• 发表时间: 2013
• 期刊: Algebraic & Geometric Topology
• 影响因子: 0.7
• 作者: Baker K