Convergent evolution of MutS and topoisomerase II for clamping DNA crossovers and stacked Holliday junctions

Protein Fold Usages in Ribosomes: Another Glance to the Past

The analysis of protein fold usage, similar to codon usage, offers profound insights into the evolution of biological systems and the origins of modern proteomes. While previous studies have examined fold distribution in modern genomes, our study focuses on the comparative distribution and usage of protein folds in ribosomes across bacteria, archaea, and eukaryotes. We identify the prevalence of certain 'super-ribosome folds,' such as the OB fold in bacteria and the SH3 domain in archaea and eukaryotes. The observed protein fold distribution in the ribosomes announces the future power-law distribution where only a few folds are highly prevalent, and most are rare. Additionally, we highlight the presence of three copies of proto-Rossmann folds in ribosomes across all kingdoms, showing its ancient and fundamental role in ribosomal structure and function. Our study also explores early mechanisms of molecular convergence, where different protein folds bind equivalent ribosomal RNA structures in ribosomes across different kingdoms. This comparative analysis enhances our understanding of ribosomal evolution, particularly the distinct evolutionary paths of the large and small subunits, and underscores the complex interplay between RNA and protein components in the transition from the RNA world to modern cellular life. Transcending the concept of folds also makes it possible to group a large number of ribosomal proteins into five categories of urfolds or metafolds, which could attest to their ancestral character and common origins. This work also demonstrates that the gradual acquisition of extensions by simple but ordered folds constitutes an inexorable evolutionary mechanism. This observation supports the idea that simple but structured ribosomal proteins preceded the development of their disordered extensions.

SCREW MOTION OF DNA DUPLEX DURING TRANSLOCATION THROUGH PORE I: INTRODUCTION OF THE COARSE-GRAINED MODEL

Based upon the structural properties of DNA duplexes and their counterion-water surrounding in solution, we have introduced here a screw model which may describe translocation of DNA duplexes through artificial nanopores of the proper diameter (where the DNA counterion–hydration shell can be intact) in a qualitatively correct way. This model represents DNA as a kind of "screw," whereas the counterion-hydration shell is a kind of "nut." Mathematical conditions for stable dynamics of the DNA screw model are investigated in detail. When an electrical potential is applied across an artificial membrane with a nanopore, the "screw" and "nut" begin to move with respect to each other, so that their mutual rotation is coupled with their mutual translation. As a result, there are peaks of electrical current connected with the mutual translocation of DNA and its counterion–hydration shell, if DNA is possessed of some non-regular base-pair sequence. The calculated peaks of current strongly resemble those observed in the pertinent experiments. An analogous model could in principle be applied to DNA translocation in natural DNA–protein complexes of biological interest, where the role of "nut" would be played by protein-tailored "channels." In such cases, the DNA screw model is capable of qualitatively explaining chemical-to-mechanical energy conversion in DNA–protein molecular machines via symmetry breaking in DNA–protein friction.

Local sensing of global DNA topology: from crossover geometry to type II topoisomerase processivity

Type II topoisomerases are ubiquitous enzymes that control the topology and higher order structures of DNA. Type IIA enzymes have the remarkable property to sense locally the global DNA topology. Although many theoretical models have been proposed, the molecular mechanism of chiral discrimination is still unclear. While experimental studies have established that topoisomerases IIA discriminate topology on the basis of crossover geometry, a recent single-molecule experiment has shown that the enzyme has a different processivity on supercoiled DNA of opposite sign. Understanding how cross-over geometry influences enzyme processivity is, therefore, the key to elucidate the mechanism of chiral discrimination. Analysing this question from the DNA side reveals first, that the different stability of chiral DNA cross-overs provides a way to locally sense the global DNA topology. Second, it shows that these enzymes have evolved to recognize the G- and T-segments stably assembled into a right-handed cross-over. Third, it demonstrates how binding right-handed cross-overs across their large angle imposes a different topological link between the topoIIA rings and the plectonemes of opposite sign thus directly affecting the enzyme freedom of motion and processivity. In bridging geometry and kinetic data, this study brings a simple solution for type IIA topoisomerase chiral discrimination.

Impact of mutS inactivation on foreign DNA acquisition by natural transformation in Pseudomonas stutzeri

In prokaryotic mismatch repair the MutS protein and its homologs recognize the mismatches. The mutS gene of naturally transformable Pseudomonas stutzeri ATCC 17587 (genomovar 2) was identified and characterized. The deduced amino acid sequence (859 amino acids; 95.6 kDa) displayed protein domains I to IV and a mismatch-binding motif similar to those in MutS of Escherichia coli. A mutS::aac mutant showed 20- to 163-fold-greater spontaneous mutability. Transformation experiments with DNA fragments of rpoB containing single nucleotide changes (providing rifampin resistance) indicated that mismatches resulting from both transitions and transversions were eliminated with about 90% efficiency in mutS+. The mutS+ gene of strain ATCC 17587 did not complement an E. coli mutant but partially complemented a P. stutzeri JM300 mutant (genomovar 4). The declining heterogamic transformation by DNA with 0.1 to 14.6% sequence divergence was partially alleviated by mutS::aac, indicating that there was a 14 to 16% contribution of mismatch repair to sexual isolation. Expression of mutS+ from a multicopy plasmid eliminated autogamic transformation and greatly decreased heterogamic transformation, suggesting that there is strong limitation of MutS in the wild type for marker rejection. Remarkably, mutS::aac altered foreign DNA acquisition by homology-facilitated illegitimate recombination (HFIR) during transformation, as follows: (i) the mean length of acquired DNA was increased in transformants having a net gain of DNA, (ii) the HFIR events became clustered (hot spots) and less dependent on microhomologies, which may have been due to topoisomerase action, and (iii) a novel type of transformants (14%) had integrated foreign DNA with no loss of resident DNA. We concluded that in P. stutzeri upregulation of MutS could enforce sexual isolation and downregulation could increase foreign DNA acquisition and that MutS affects mechanisms of HFIR.

The Arabidopsis MutS homolog AtMSH4 functions at an early step in recombination: evidence for two classes of recombination in Arabidopsis

MSH4, a meiosis-specific member of the MutS-homolog family of genes, is required for normal levels of recombination and fertility in budding yeast, mouse, and Caenorhabditis elegans. In this paper, we report the identification and characterization of the Arabidopsis homolog of MSH4 (AtMSH4). We demonstrate that AtMSH4 expression can only be detected in floral tissues, consistent with a role in reproduction. Immunofluorescence studies indicate that its expression is limited to early meiotic prophase I, preceding the synapsis of homologous chromosomes. A T-DNA insertional mutant (Atmsh4) exhibited normal vegetative growth but a severe reduction in fertility, consistent with a meiotic defect; this was confirmed by cytological analysis of meiosis. RNAi-induced down-regulation of the MSH4 gene resulted in a similar fertility and meiotic phenotype. We demonstrate that prophase I chromosome synapsis is delayed and may be incomplete in Atmsh4, and metaphase I chiasma frequency is greatly reduced to approximately 15% of wild type, leading to univalence and nondisjunction. We show that these residual chiasmata are randomly distributed among cells and chromosomes. These features of chiasma frequency and distribution in Atmsh4 show close parallels to MSH4-independent crossovers in budding yeast that have been proposed to originate by a separate pathway. Furthermore, the characteristics of the MSH4-independent chiasmata in the Atmsh4 mutant closely parallel those of second-pathway crossovers that have been postulated from Arabidopsis crossover analysis and mathematical modeling. Taken together, this evidence strongly indicates that Arabidopsis possesses two crossover pathways.