Rescuing a sinking ship: The role of recombination gene products in SOS induction in Escherichia coli

In Escherichia coli (E. coli) DNA damage is repaired by the process of homologous recombination (HR). There are two main types of DNA damage, double-stranded (ds) DNA breaks (DSBs) and single-stranded (ss) DNA gaps (SSGs). DSBs can arise from external DNA-damaging agents, from induction of specific endonucleases which introduce DSBs in a specific recognition site, or due to endogenous DNA damage. SSGs are formed after replication of UV irradiated E. coli cells. Both types of DNA damage, DSBs and SSGs, induce the SOS response which includes elevated expression of genes whose products are involved in DNA metabolism, inhibition of cell division and prophage induction. DSBs are repaired by the RecBCD pathway of recombination, whereas SSGs are repaired by the RecF recombination pathway. Proteins in both recombinaton pathways, i.e., RecBCD and RecF, act to produce the recombinogenic RecA filament which is crucial for recombinational DNA repair and induction of the SOS response. It is known that the inactivation of some recombination gene products can lead to an impaired SOS response. Here we review the roles of recombination proteins in the formation of a RecA filament and in the induction of a SOS response

Dominantna epistaza između dva lokusa kvantitativnog svojstva učinkovitosti sporulacije kvasca Saccharomyces cerevisiae

Sporulation efficiency in the yeast Saccharomyces cerevisiae is a well-established model for studying quantitative traits. A variety of genes and nucleotides causing different sporulation efficiencies in laboratory, as well as in wild strains, has already been extensively characterised (mainly by reciprocal hemizygosity analysis and nucleotide exchange methods). We applied a different strategy in order to analyze the variation in sporulation efficiency of laboratory yeast strains. Coupling classical quantitative genetic analysis with simulations of phenotypic distributions (a method we call phenotype modelling) enabled us to obtain a detailed picture of the quantitative trait loci (QTLs) relationships underlying the phenotypic variation of this trait. Using this approach, we were able to uncover a dominant epistatic inheritance of loci governing the phenotype. Moreover, a molecular analysis of known causative quantitative trait genes and nucleotides allowed for the detection of novel alleles, potentially responsible for the observed phenotypic variation. Based on the molecular data, we hypothesise that the observed dominant epistatic relationship could be caused by the interaction of multiple quantitative trait nucleotides distributed across a 60-kb QTL region located on chromosome XIV and the RME1 locus on chromosome VII. Furthermore, we propose a model of molecular pathways which possibly underlie the phenotypic variation of this trait.Učinkovitost sporulacije često se koristi za proučavanje kvantitativnih svojstava kvasca Saccharomyces cerevisiae. Velik broj gena i nukleotida koji utječu na učinkovitost sporulacije kvasca u laboratorijskim te divljim sojevima temeljito je okarakteriziran (uglavnom pomoću tehnike recipročne hemizigotnosti i ciljanom izmjenom nukleotida). U ovom smo radu primijenili drukčiju strategiju analize učinkovitosti sporulacije laboratorijskih sojeva kvasca. Povezivanjem klasičnih analiza kvantitativne genetike sa simulacijama fenotipskih distribucija (metoda modeliranja fenotipova) omogućena je detaljna analiza genetičkih odnosa između lokusa kvantitativnog svojstva učinkovitosti sporulacije. Na taj smo način otkrili dominantno epistatski odnos između dva lokusa koji pridonose učinkovitosti sporulacije. Štoviše, molekularna analiza poznatih gena i nukleotida što utječu na sporulaciju omogućila je pronalazak novih alela, koji su vjerojatno odgovorni za fenotipsku varijaciju. Pretpostavljamo da je dominantno epistatski način nasljeđivanja učinkovitosti sporulacije rezultat interakcije regije DNA na kromosomu XIV, duge 60 kb, te lokusa RME1 na kromosomu VII. Nadalje, predlažemo model pomoću kojeg se mogu opisati signalni putevi što reguliraju učinkovitost sporulacije

Simultaneous plasmid integration: a unifying model of multiple plasmid integration into the yeast chromosome

Recombination of non-replicative plasmids bearing yeast homology with the chromosome can integrate the plasmid molecule into the genome. Such process is also known to integrate more than one plasmid molecule leading to multiple, tandem plasmid integration. However, its exact molecular mechanism remains unknown. There are two alternative models to explain such integration. The first predicts single integration of a super-plasmid molecule and the second sequential integration of several independent molecules, but neither is able to comprehend all experimental data. Therefore, here is presented a theoretical model that unifies both prior models owing to the possibility that two plasmid molecules recombine with the chromosome simultaneously. This model was used as a theoretical tool in order to discriminate between existing alternatives extracting the sequential model as a better overall explanation

Genetička analiza produkata bakterije Escherichia coli koji sudjeluju u konjugacijskoj rekombinaciji u prisutnosti proteina Gam faga λ

The Gam protein of phage is a well-known inhibitor of the enzymatic activities of the RecBCD enzyme, the major enzyme involved in homologous recombination in bacteria Escherichia coli. In this work, we studied (i) the effect of the RecA loading-deficient recB (recBD1080A) mutation on conjugational recombination in the presence of phage Gam protein and (ii) additional genetic requirements for the RecBCD-Gam-mediated conjugational recombination. For this purpose, we introduced Gam+ and Gam- expressing plasmids into wild type cells and different mutants of E. coli (recJ, recBD1080A, recB, recN, recF, recR, recO, recD), and determined the yields of recombinants after Hfr mediated conjugation. The obtained results suggest that RecA loading activity is not inhibited by Gam and that conjugational recombination in the presence of Gam is partially dependent on recJ and recO gene products.Gam protein bakteriofaga λ je inhibitor enzimskih aktivnosti enzima RecBCD koji sudjeluje u homolognoj genetičkoj rekombinaciji u bakteriji Escherichia coli. U ovom su radu proučavani (i) učinak recB mutacije deficijentne u nanošenju proteina RecA (recBD1080A) na konjugacijsku rekombinaciju u prisutnosti proteina Gam faga λ i (ii) učinak mutacija drugih rekombinacijskih gena na konjugacijsku rekombinaciju u bakterijama s kompleksom RecBCD-Gam. Zbog toga smo unijeli plazmide koji eksprimiraju Gam+ i Gam– u divlji tip i u različite mutante bakterije Escherichia coli (recJ, recBD1080A, recB, recN, recF, recR, recO, recD), te odredili prinos rekombinanata nakon Hfr-konjugacije. Dobiveni su rezultati pokazali da aktivnost nanošenja proteina RecA vjerojatno nije inhibirana proteinom Gam. U prisutnosti proteina Gam konjugacijska rekombinacija djelomično ovisi o produktima gena recJ i recO

Quantitative Genetics and Evolution

Today, evolution is a unifying concept in biology. A century and half ago, Darwin developed the theory of natural selection, and proposed it as the mainmechanism of evolution. A quantitative approach to the study of evolution required new theoretical developments in population and quantitative genetics. Here, I review the basic concepts of quantitative genetics neccessary to understand microevolutionary change. Natural selection is a consequence of differences in fitness (reproductive success) between individuals in a population. But natural selection is not equal to evolution. In order to achieve evolutionary change, variation in fitness must be heritable, i. e. it must be transmited by genes from parents to offspring. Besides fitness differences, individuals within a population often differ in many other characters (morphological, physiological and behavioural) which are also genetically transmited from generation to generation. It is crucial to distinguish the process of selection which operates in an existing generation from the evolutionary change which is visible in the next generation. Most concepts of quantitative genetics centre around variances and covariances, and include the evolutionary potential of a population or heritability (ratio of additive genetic variance and phenotypic variance), the strength of selection on a particular trait (covariance of particular trait and fitness), the total strength of selection (phenotypic variance in fitness) and evolutionary response (phenotypic change in the next generation) which can be predicted by breeder’s equation

Rescuing a sinking ship: The role of recombination gene products in SOS induction in Escherichia coli

In Escherichia coli (E. coli) DNA damage is repaired by the process of homologous recombination (HR). There are two main types of DNA damage, double-stranded (ds) DNA breaks (DSBs) and single-stranded (ss) DNA gaps (SSGs). DSBs can arise from external DNA-damaging agents, from induction of specific endonucleases which introduce DSBs in a specific recognition site, or due to endogenous DNA damage. SSGs are formed after replication of UV irradiated E. coli cells. Both types of DNA damage, DSBs and SSGs, induce the SOS response which includes elevated expression of genes whose products are involved in DNA metabolism, inhibition of cell division and prophage induction. DSBs are repaired by the RecBCD pathway of recombination, whereas SSGs are repaired by the RecF recombination pathway. Proteins in both recombinaton pathways, i.e., RecBCD and RecF, act to produce the recombinogenic RecA filament which is crucial for recombinational DNA repair and induction of the SOS response. It is known that the inactivation of some recombination gene products can lead to an impaired SOS response. Here we review the roles of recombination proteins in the formation of a RecA filament and in the induction of a SOS response