Modes of Escherichia coli Dps Interaction with DNA as Revealed by Atomic Force Microscopy

Abstract

Multifunctional protein Dps plays an important role in iron assimilation and a crucial role in bacterial genome packaging. Its monomers form dodecameric spherical particles accumulating ~400 molecules of oxidized iron ions within the protein cavity and applying a flexible N-terminal ends of each subunit for interaction with DNA. Deposition of iron is a well-studied process by which cells remove toxic Fe2+ ions from the genetic material and store them in an easily accessible form. However, the mode of interaction with linear DNA remained mysterious and binary complexes with Dps have not been characterized so far. It is widely believed that Dps binds DNA without any sequence or structural preferences but several lines of evidence have demonstrated its ability to differentiate gene expression, which assumes certain specificity. Here we show that Dps has a different affinity for the two DNA fragments taken from the dps gene regulatory region. We found by atomic force microscopy that Dps predominantly occupies thermodynamically unstable ends of linear double-stranded DNA fragments and has high affinity to the central part of the branched DNA molecule self-assembled from three single-stranded oligonucleotides. It was proposed that Dps prefers binding to those regions in DNA that provide more contact pads for the triad of its DNA-binding bundle associated with one vertex of the protein globule. To our knowledge, this is the first study revealed the nucleoid protein with an affinity to branched DNA typical for genomic regions with direct and inverted repeats. As a ubiquitous feature of bacterial and eukaryotic genomes, such structural elements should be of particular care, but the protein system evolutionarily adapted for this function is not yet known, and we suggest Dps as a putative component of this system.

The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner

“…An ability to bind and condense genomic DNA is a specific feature of proteins from the Dps-family [ 18 ]. Both inner [ 5 ] and outer [ 5 , 19 ] surfaces of the E . coli Dps are charged negatively, thus it is not clear how this protein was evolutionary selected for interaction with negatively charged DNA.…”

“…These changes were explained by the lack of Dps-mediated global structural impact on the bacterial chromosome or by regulatory effects from transcription factors, occupying the sites occasionally bound by Dps and released in its absence. For all that, genomic SELEX revealed sequences that were preferably bound by Dps in vitro (data deposited in DataBase TEC https://shigen.nig.ac.jp/ecoli/tec/top/about [ 35 ]), and we detected an ability of Dps to choose one of the two competing DNA fragments for complex formation [ 19 ]. Dps, therefore, may have some sequence or structural selectivity.…”

“…Dps, therefore, may have some sequence or structural selectivity. Some preference of Dps for the ends of linear DNA fragments and even higher affinity for the branching point of artificial 3-way junction molecules was detected by atomic force microscopy [ 19 ]. Based on these data, it was assumed that Dps tends to bind those sites in the genomic DNA, which have locally increased “concentration” of DNA providing a platform for the maximal number of N-termini.…”

Bacterial nucleoid protein Dps binds structured RNA molecules

“…Стало очевидно, что эффективнее всего с Dps связываются транспортные и малые регуляторные РНК. Все такие молекулы формируют стабильные шпилечные структуры, что подтверждает предположение о повышенном сродстве Dps к разветвлённым структурам в нуклеиновых кислотах [14]. Кроме этого, в комплексе с Dps было обнаружено семь РНК-продуктов, синтезируемых из межгенных участков (отмечены красным в таблице 1).…”

“…Несмотря на электростатическую природу связывания, эффективность взаимодействия с разными фрагментами ДНК может отличаться [14], что свидетельствуют о некоторой селективности белка. Согласно данным, полученным методом атомно-силовой микроскопии, эта избирательность может быть обусловлена повышенным сродством Dps к разветвлённым структурам в ДНК [14]. Такие участки предоставляют возможность для образования множественных контактов с N-концевыми модулями белка, что неизбежно стабилизирует взаимодействие.…”