Brézellec Pierre, Hoebeke Mark, Hiet Marie-Sophie, Pasek Sophie, Ferat Jean-Luc
Laboratoire Statistique et Génome du CNRS, Tour Evry 2, 523, Place des Terrasses de l'Agora, 91034 Evry Cedex, France.
Bioinformatics. 2006 Aug 15;22(16):1935-41. doi: 10.1093/bioinformatics/btl336. Epub 2006 Jun 20.
The Dam methyltransferase (DamMT) activity, broadly distributed in association with restriction endonucleases, as part of the restriction-modification defense systems, has evolved to become intimately associated with essential biological functions in a few organisms. In Escherichia coli, DamMT is involved in multiple aspects of DNA maintenance, replication initiation, daughter chromosome segregation, DNA mismatch repair, gene expression control, etc. The participation of DamMT in such a diverse set of functions required that other genes adapted, or emerged through evolution, in response to the DamMT-induced modification of the genomic environment. One example is SeqA, a protein that senses the methylation status of the origin of replication of the chromosome to control the timing of replication initiation. Interestingly, seqA is only present in a few DamMT-specifying proteobacteria. This observation led us to hypothesize that other genes, specifying related functions, might also be found in these organisms. To test this hypothesis, we implemented a large-scale comparative genomic screen meant to identify genes specifying DNA methylation sensing domains, probably involved in DNA maintenance functions.
We carried out a phylogenetic analysis of DamMT, identifying two contrasting behaviors of the protein. Based on this phylogeny, we defined precisely a set of genomes, in which the protein activity is likely to be involved in DNA maintenance functions, the 'resident' dam genomes. We defined a second set of genomes, in which DamMT is not resident. We developped a new tool, 'DomainSieve', in order to screen these two sets for protein domains that are strictly associated with 'resident' dam genomes. This approach was rewarding and generated a list of genes, among which some, at least, specify activities with clear linkage to DamMT-dependent DNA methylation and DNA maintenance.
DomainSieve is implemented as a web resource and is accessible at http://stat.genopole.cnrs.fr/ds/.
Dam甲基转移酶（DamMT）活性广泛分布，与限制内切酶相关联，作为限制修饰防御系统的一部分，在一些生物体中已进化为与基本生物学功能密切相关。在大肠杆菌中，DamMT参与DNA维持、复制起始、子染色体分离、DNA错配修复、基因表达控制等多个方面。DamMT参与如此多样的功能要求其他基因适应或通过进化出现，以应对DamMT诱导的基因组环境修饰。一个例子是SeqA，一种感知染色体复制起点甲基化状态以控制复制起始时间的蛋白质。有趣的是，seqA仅存在于少数指定DamMT的变形菌中。这一观察结果使我们推测，在这些生物体中可能还会发现其他指定相关功能的基因。为了验证这一假设，我们实施了一项大规模比较基因组筛选，旨在识别指定可能参与DNA维持功能的DNA甲基化传感结构域的基因。
我们对DamMT进行了系统发育分析，确定了该蛋白质的两种不同行为。基于此系统发育，我们精确地定义了一组基因组，其中蛋白质活性可能参与DNA维持功能，即“常驻”dam基因组。我们定义了第二组基因组，其中DamMT并非常驻。我们开发了一种新工具“DomainSieve”，以便在这两组基因组中筛选与“常驻”dam基因组严格相关的蛋白质结构域。这种方法很有成效，并生成了一份基因列表，其中至少有一些基因指定的活性与DamMT依赖的DNA甲基化和DNA维持有明确联系。
DomainSieve作为一个网络资源实现，可在http://stat.genopole.cnrs.fr/ds/访问。
