Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain

Recently, a multiple gene cassette with mutagenic translation synthesis activity was identified and shown to be under LexA regulation in several proteobacteria species. In this work, we have traced down instances of this multiple gene cassette across the bacteria domain. Phylogenetic analyses show that this cassette has undergone several reorganizations since its inception in the actinobacteria, and that it has dispersed across the bacterial domain through a combination of vertical inheritance, lateral gene transfer and duplication. In addition, our analyses show that LexA regulation of this multiple gene cassette is persistent in all the phyla in which it has been detected, and suggest that this regulation is prompted by the combined activity of two of its constituent genes: a polymerase V homolog and an alpha subunit of the DNA polymerase III

Reconstruction of the evolutionary history of the LexA-binding sequence

In recent years, the recognition sequence of the SOS repressor LexA protein has been identified for several bacterial clades, such as the Gram-positive, green non-sulfur bacteria and Cyanobacteria phyla, or the 'Alphaproteobacteria', 'Deltaproteobacteria' and 'Gammaproteobacteria' classes. Nevertheless, the evolutionary relationship among these sequences and the proteins that recognize them has not been analysed. Fibrobacter succinogenes is an anaerobic Gram-negative bacterium that branched from a common bacterial ancestor immediately before the Proteobacteria phylum. Taking advantage of its intermediate position in the phylogenetic tree, and in an effort to reconstruct the evolutionary history of LexA-binding sequences, the F. succinogenes lexA gene has been isolated and its product purified to identify its DNA recognition motif through electrophoretic mobility assays and footprinting experiments. After comparing the available LexA DNA-binding sequences with the F. succinogenes one, reported here, directed mutagenesis of the F. succinogenes LexA-binding sequence and phylogenetic analyses of LexA proteins have revealed the existence of two independent evolutionary lanes for the LexA recognition motif that emerged from the Gram-positive box: one generating the Cyanobacteria and 'Alphaproteobacteria' LexA-binding sequences, and the other giving rise to the F. succinogenes and Myxococcus xanthus ones, in a transitional step towards the current 'Gammaproteobacteria' LexA box. The contrast between the results reported here and the phylogenetic data available in the literature suggests that, some time after its emergence as a distinct bacterial class, the 'Alphaproteobacteria' lost its vertically received lexA gene, but received later through lateral gene transfer a new lexA gene belonging to either a cyanobacterium or a bacterial species closely related to this phylum. This constitutes the first report based on experimental evidence of lateral gene transfer in the evolution of a gene governing such a complex regulatory network as the bacterial SOS system

Evolució del motiu d'unió de la proteïna LexA al Domini Bacteria

Consultable des del TDXTítol obtingut de la portada digitalitzadaEl sistema SOS és una xarxa multigénico induïble davant del dany al DNA. Les seves funcions estan relacionades amb la replicació, reparació del DNA, mutagènesi I control del cicle cel·lular. Aquesta xarxa ha estat caracteritzada per diferents bacteris grampositius i gramnegatius, trobant-se per a tots ells un motiu d'unió del seu repressor, la proteïna LexA. El present treball de Tesi es centra en la caracterització del motiu d'unió de la proteïna LexA a Xylella fastidiosa, Anabaena sp. i Fibrobacter succinogenes. Mitjançant recerques amb el programa TBLASTN, els gens lexA d'aquests microorganismes han estat identificats. Després de procedir a la seva clonació, els productes que codifiquen han estat expressats I purificats mitjançant sistemes d'afinitat a la cua d'histidines o a la GST. Assaigs de mobilitat electroforética i de footprinting utilitzant el promotor de lexA i proteïna purificada, ens han permès definir el motiu d'unió de la proteïna LexA a tots tres microorganismes: TTAGN6TACTA per a X. fastidiosa, RGTACNNNDGTWCB per a Anabaena i TGCNCN4GTGCA per a F. succinogenes. Aquests motius d'unió han estat utilitzats per determinar la composició del reguló LexA a l'ordre Xanthomonadals i als phyla Cianobacteris i Fibrobacter. Aquest estudi ens ha permès descriure una important variabilitat en la composició d'aquests regulons i la presència de gens induïbles davant del dany al DNA de manera independent de LexA a X.fastidiosa. Estudis de mutagènesis dirigida utilitzant les seqüències d'unió de la proteïna LexA a Anabaena i F. succinogenes i estudis filogenètics amb les proteïnes LexA i RecA ens han permès determinar la història evolutiva del motiu d'unió de LexA al Domini Bacteria, demostrant que a la subdivisió 'Alphaproteobacteria' s'ha perdut la còpia del gen lexA heretada verticalment essent la que presenten actualment aquests bacteris una adquisició per transferència horitzontal a partir d'un ancestre d'una cianobactèria o espècie relacionada. Els següents articles donen suport a les dades i conclusions del treball, que ha estat redactat com a compendi d'aquestes publicacions : Campoy, S., Mazón, G., Fernández de Henestrosa, A.R., Llagostera, M., Monteiro, P.B. i Barbé, J. 2002. A new regulatory DNA motif of the gamma subclass Proteobacteria: identification of the LexA protein binding site of the plant pathogen Xylella fastidiosa. Microbiology 148: 3583 - 3597. Mazón G., Lucena J.M., Campoy, S., Fernández de Henestrosa, A.R., Candau, P. i Barbé J. 2004. LexA-binding sequence in Gram-positive and cyanobacteria are closely related. Mol. Gen. Genomics 271: 40 - 49. Mazón, G., Erill, I., Campoy, S., Cortés, P., Forano, E. i Barbé, J. 2004. Reconstruction of the evolutionary history of the LexA binding sequence. Microbiology 150: 3783-3795.The SOS network is a DNA-damage inducible multigenic network whose functions are involved in DNA replication, DNA repair, mutagenesis and control of cell cycle. This network has been characterized in different gram-positive and gram-negative bacterial species. A binding-motif for their repressor, the LexA protein, has been already determined. The present work focuses in the characterization of the LexA-binding motif of Xylella fastidiosa, Anabaena sp. and Fibrobacter succinogenes. Using TBLASTN searches, their respective lexA genes have been identified and cloned, and their products expressed and purified using histidine-tag and GST-tag systems. Electrophoretic mobility shift assays and foot-printing experiments performed using purified LexA proteins and their lexA promoter fragments revealed the presence of the specific LexA-binding motif for these microorganisms: TTAGN6TACTA for X. fastidiosa, RGTACNNNDGTWCB for Anabaena and TGCNCN4GTGCA for F. succinogenes. These three binding motifs have been used to elucidate the LexA regulon composition in the Order Xanthomonadales and the Cyanobacteria and Fibrobacter phyla, showing an important variability in their regulon composition and the presence of LexA-independent DNA-damage inducible genes in X. fastidiosa. Directed mutagenesis of the Anabaena and F. succinogenes LexA-binding sequences and phylogenetic analyses of LexA and RecA proteins have revealed the evolutionary history of the LexA-binding motif in the Bacteria Domain, with the loss of the vertically inherited lexA gene in 'Alphaproteobacteria' and the presence of a lateral gene transfer in these group resulting in a new lexA copy acquired from a cyanobacterium ancestor or related species. This work is supported on data published in the following papers: Campoy, S., Mazón, G., Fernández de Henestrosa, A.R., Llagostera, M., Monteiro, P.B. i Barbé, J. 2002. A new regulatory DNA motif of the gamma subclass Proteobacteria: identification of the LexA protein binding site of the plant pathogen Xylella fastidiosa. Microbiology 148: 3583 - 3597. Mazón G., Lucena J.M., Campoy, S., Fernández de Henestrosa, A.R., Candau, P. i Barbé J. 2004. LexA-binding sequence in Gram-positive and cyanobacteria are closely related. Mol. Gen. Genomics 271: 40 - 49. Mazón, G., Erill, I., Campoy, S., Cortés, P., Forano, E. i Barbé, J. 2004. Reconstruction of the evolutionary history of the LexA binding sequence. Microbiology 150: 3783-3795

SUMO-mediated recruitment allows timely function of the Yen1 nuclease in mitotic cells

International audienceThe post-translational modification of DNA damage response proteins with SUMO is an important mechanism to orchestrate a timely and orderly recruitment of repair factors to damage sites. After DNA replication stress and double-strand break formation, a number of repair factors are SUMOylated and interact with other SUMOylated factors, including the Yen1 nuclease. Yen1 plays a critical role in ensuring genome stability and unperturbed chromosome segregation by removing covalently linked DNA intermediates between sister chromatids that are formed by homologous recombination. Here we show how this important role of Yen1 depends on interactions mediated by non-covalent binding to SUMOylated partners. Mutations in the motifs that allow SUMO-mediated recruitment of Yen1 impair its ability to resolve DNA intermediates and result in chromosome mis-segregation and increased genome instability

Sumo-mediated recruitment allows timely function of the Yen1 nuclease in mitotic cells

Abstract The modification of DNA damage response proteins with Sumo is an important mechanism to orchestrate a timely and orderly recruitment of repair factors to damaged sites. After replication stress and double-strand break formation a number of repair factors are Sumoylated and interact with other Sumoylated factors, including the nuclease Yen1. Yen1 plays a critical role to ensure genome stability and unperturbed chromosome segregation by removing covalently linked DNA intermediates that are formed by homologous recombination. Here we show how this important role of Yen1 is dependent on interactions mediated by non-covalent binding to Sumoylated partners. Mutations in the motifs that allow Sumo-mediated recruitment of Yen1 impair its ability to resolve DNA intermediates and result in increased genome instability and chromosome mis-segregation

Running Title: Evolution of the LexA binding sequence

In recent years, the recognition sequence of the SOS repressor LexA protein has been identified for several bacterial clades, such as the Gram-positive, Green-non Sulfur bacteria and Cyanobacteria phyla, or the Alpha, Delta and Gamma Proteobacteria classes. Nevertheless, the evolutionary relationship among these sequences and the proteins that recognize them has not been analyzed. Fibrobacter succinogenes is an anaerobic Gram-negative bacterium that branched from a common bacterial ancestor immediately before the Proteobacteria phylum. Taking advantage of its intermediate position in the phylogenetic tree, and in an effort to reconstruct the evolutionary history of LexA binding sequences, the F. succinogenes lexA gene has been isolated and its product purified to identify its DNA recognition motif through electrophoretic mobility assays and footprinting experiments. After comparing the available LexA DNA binding sequences with the here reported F. succinogenes one, directed mutagenesis of the F. succinogenes LexA binding sequence and phylogenetic analyses of LexA proteins have revealed the existence of two independent evolutionary lanes for the LexA recognition motif that emerged from the Gram