Transposable elements: Uniqueness and applications

@#The study of transposable genetic elements, a cornerstone of molecular genetics, offers profound insights into the dynamic nature of genetic material. This exploration encompasses various types found in bacteria, including insertion sequences, composite and non-composite transposons. These elements are instrumental in shaping bacterial genomes by facilitating the movement of genetic information, driving evolution and contributing to genetic diversity. Understanding the mechanisms of transposition is essential for unravelling the intricate processes governing genetic rearrangements. Replicative and conservative transposition mechanisms, exemplified by the Tn3 family and phage Mu, illustrate the remarkable adaptability of these systems in reshaping genomes. However, it is the transposon Tn5 that steals the spotlight as a versatile molecular genetics tool. Tn5's transposition mechanism, characterized by precise control over gene expression, translational regulation, protein localization and the induction of conditional mutations, empowers researchers to dissect gene regulation intricacies with unprecedented accuracy. Transposable genetic elements, epitomized by Tn5, are indispensable instruments in molecular genetics. They allow researchers to navigate the intricate landscape of genetics, exploring gene regulation, protein function, and genetic diversity with unparalleled precision. These elements continue to be at the forefront of molecular genetics research, driving innovations that deepen our understanding of the fundamental mechanisms governing life's genetic code.

The progress of research on transposons in diagnosis and treatment of urological malignancies / 中华泌尿外科杂志

Transposons are the most prevalent elements in human genomes, which plays a vital role in gene expression regulation and evolutionary processes. They also jeopardize genome integrity with the characteristics of jumping and insertions. A delicate balance is maintained between the benefits and deleterious aspects of transposons, mediated by the epigenetic regulatory system. Once the balance is broken, it will give rise to genomic instability, leading to neoplasia. A lot of studies have shown that the transcriptional activation, expression products and methylation of transposons are closely related with urological malignancies, holding tremendous potential as biomarkers for risk and effect prediction, noninvasive diagnosis and targeted therapies of urological malignancies. In this article, the molecular mechanisms of transposons underlying the initiation, promotion and progression of urological malignancies as well as advances in diagnosis and treatment are reviewed.

Era-like GTP protein gene expression in rice / Expressão do gene da proteína GTP semelhante à era no arroz

The mutations are genetic changes in the genome sequences and have a significant role in biotechnology, genetics, and molecular biology even to find out the genome sequences of a cell DNA along with the viral RNA sequencing. The mutations are the alterations in DNA that may be natural or spontaneous and induced due to biochemical reactions or radiations which damage cell DNA. There is another cause of mutations which is known as transposons or jumping genes which can change their position in the genome during meiosis or DNA replication. The transposable elements can induce by self in the genome due to cellular and molecular mechanisms including hypermutation which caused the localization of transposable elements to move within the genome. The use of induced mutations for studying the mutagenesis in crop plants is very common as well as a promising method for screening crop plants with new and enhanced traits for the improvement of yield and production. The utilization of insertional mutations through transposons or jumping genes usually generates stable mutant alleles which are mostly tagged for the presence or absence of jumping genes or transposable elements. The transposable elements may be used for the identification of mutated genes in crop plants and even for the stable insertion of transposable elements in mutated crop plants. The guanine nucleotide-binding (GTP) proteins have an important role in inducing tolerance in rice plants to combat abiotic stress conditions.

Mutações são alterações genéticas nas sequências do genoma e têm papel significativo na biotecnologia, genética e biologia molecular, até mesmo para descobrir as sequências do genoma de um DNA celular junto com o sequenciamento do RNA viral. As mutações são alterações no DNA que podem ser naturais ou espontâneas e induzidas devido a reações bioquímicas ou radiações que danificam o DNA celular. Há outra causa de mutações, conhecida como transposons ou genes saltadores, que podem mudar sua posição no genoma durante a meiose ou a replicação do DNA. Os elementos transponíveis podem induzir por si próprios no genoma devido a mecanismos celulares e moleculares, incluindo hipermutação que causou a localização dos elementos transponíveis para se moverem dentro do genoma. O uso de mutações induzidas para estudar a mutagênese em plantas cultivadas é muito comum, bem como um método promissor para a triagem de plantas cultivadas com características novas e aprimoradas para a melhoria da produtividade e da produção. A utilização de mutações de inserção por meio de transposons ou genes saltadores geralmente gera alelos mutantes estáveis que são marcados quanto à presença ou ausência de genes saltadores ou elementos transponíveis. Os elementos transponíveis podem ser usados para a identificação de genes mutados em plantas de cultivo e até mesmo para a inserção estável de elementos transponíveis em plantas de cultivo mutadas. As proteínas de ligação ao nucleotídeo guanina (GTP) têm papel importante na indução de tolerância em plantas de arroz para combater as condições de estresse abiótico.

Era-like GTP protein gene expression in rice

Abstract The mutations are genetic changes in the genome sequences and have a significant role in biotechnology, genetics, and molecular biology even to find out the genome sequences of a cell DNA along with the viral RNA sequencing. The mutations are the alterations in DNA that may be natural or spontaneous and induced due to biochemical reactions or radiations which damage cell DNA. There is another cause of mutations which is known as transposons or jumping genes which can change their position in the genome during meiosis or DNA replication. The transposable elements can induce by self in the genome due to cellular and molecular mechanisms including hypermutation which caused the localization of transposable elements to move within the genome. The use of induced mutations for studying the mutagenesis in crop plants is very common as well as a promising method for screening crop plants with new and enhanced traits for the improvement of yield and production. The utilization of insertional mutations through transposons or jumping genes usually generates stable mutant alleles which are mostly tagged for the presence or absence of jumping genes or transposable elements. The transposable elements may be used for the identification of mutated genes in crop plants and even for the stable insertion of transposable elements in mutated crop plants. The guanine nucleotide-binding (GTP) proteins have an important role in inducing tolerance in rice plants to combat abiotic stress conditions.

Resumo Mutações são alterações genéticas nas sequências do genoma e têm papel significativo na biotecnologia, genética e biologia molecular, até mesmo para descobrir as sequências do genoma de um DNA celular junto com o sequenciamento do RNA viral. As mutações são alterações no DNA que podem ser naturais ou espontâneas e induzidas devido a reações bioquímicas ou radiações que danificam o DNA celular. Há outra causa de mutações, conhecida como transposons ou genes saltadores, que podem mudar sua posição no genoma durante a meiose ou a replicação do DNA. Os elementos transponíveis podem induzir por si próprios no genoma devido a mecanismos celulares e moleculares, incluindo hipermutação que causou a localização dos elementos transponíveis para se moverem dentro do genoma. O uso de mutações induzidas para estudar a mutagênese em plantas cultivadas é muito comum, bem como um método promissor para a triagem de plantas cultivadas com características novas e aprimoradas para a melhoria da produtividade e da produção. A utilização de mutações de inserção por meio de transposons ou genes saltadores geralmente gera alelos mutantes estáveis que são marcados quanto à presença ou ausência de genes saltadores ou elementos transponíveis. Os elementos transponíveis podem ser usados para a identificação de genes mutados em plantas de cultivo e até mesmo para a inserção estável de elementos transponíveis em plantas de cultivo mutadas. As proteínas de ligação ao nucleotídeo guanina (GTP) têm papel importante na indução de tolerância em plantas de arroz para combater as condições de estresse abiótico.

Era-like GTP protein gene expression in rice / Expressão do gene da proteína GTP semelhante à era no arroz

The mutations are genetic changes in the genome sequences and have a significant role in biotechnology, genetics, and molecular biology even to find out the genome sequences of a cell DNA along with the viral RNA sequencing. The mutations are the alterations in DNA that may be natural or spontaneous and induced due to biochemical reactions or radiations which damage cell DNA. There is another cause of mutations which is known as transposons or jumping genes which can change their position in the genome during meiosis or DNA replication. The transposable elements can induce by self in the genome due to cellular and molecular mechanisms including hypermutation which caused the localization of transposable elements to move within the genome. The use of induced mutations for studying the mutagenesis in crop plants is very common as well as a promising method for screening crop plants with new and enhanced traits for the improvement of yield and production. The utilization of insertional mutations through transposons or jumping genes usually generates stable mutant alleles which are mostly tagged for the presence or absence of jumping genes or transposable elements. The transposable elements may be used for the identification of mutated genes in crop plants and even for the stable insertion of transposable elements in mutated crop plants. The guanine nucleotide-binding (GTP) proteins have an important role in inducing tolerance in rice plants to combat abiotic stress conditions.

Mutações são alterações genéticas nas sequências do genoma e têm papel significativo na biotecnologia, genética e biologia molecular, até mesmo para descobrir as sequências do genoma de um DNA celular junto com o sequenciamento do RNA viral. As mutações são alterações no DNA que podem ser naturais ou espontâneas e induzidas devido a reações bioquímicas ou radiações que danificam o DNA celular. Há outra causa de mutações, conhecida como transposons ou genes saltadores, que podem mudar sua posição no genoma durante a meiose ou a replicação do DNA. Os elementos transponíveis podem induzir por si próprios no genoma devido a mecanismos celulares e moleculares, incluindo hipermutação que causou a localização dos elementos transponíveis para se moverem dentro do genoma. O uso de mutações induzidas para estudar a mutagênese em plantas cultivadas é muito comum, bem como um método promissor para a triagem de plantas cultivadas com características novas e aprimoradas para a melhoria da produtividade e da produção. A utilização de mutações de inserção por meio de transposons ou genes saltadores geralmente gera alelos mutantes estáveis que são marcados quanto à presença ou ausência de genes saltadores ou elementos transponíveis. Os elementos transponíveis podem ser usados para a identificação de genes mutados em plantas de cultivo e até mesmo para a inserção estável de elementos transponíveis em plantas de cultivo mutadas. As proteínas de ligação ao nucleotídeo guanina (GTP) têm papel importante na indução de tolerância em plantas de arroz para combater as condições de estresse abiótico.

Co-existence of blaOXA-23 and blaVIM in carbapenem-resistant Acinetobacter baumannii isolates belonging to global complex 2 in a Chinese teaching hospital / 中华医学杂志(英文版)

Background:@#Carbapenem-resistant Acinetobacter baumannii (CRAB) have been a challenging concern of health-care associated infections. The aim of the current study was to investigate the molecular epidemiology and clonal dissemination of CRAB isolates in a Chinese teaching hospital.@*Methods:@#Non-duplicate clinical A. baumannii isolates were collected from inpatients, and we measured the minimal inhibitory concentrations to determine antimicrobial susceptibility. Polymerase chain reaction (PCR) and sequencing were performed to detect carbapenem-resistance genes and occurrence of transposons among CRAB isolates. Moreover, the genetic diversity among isolates and clonal dissemination were determined by repetitive element PCR-mediated DNA fingerprinting (rep-PCR) and multilocus sequence typing (MLST).@*Results:@#A total of 67 CRAB isolates displayed resistance to most of the antibiotics tested in this study, except tigecycline. We detected blaOXA-23, blaOXA-51, blaOXA-58, and blaVIM genes in 94.0%, 100.0%, 1.5%, and 80.6% of the CRAB isolates, respectively. Nevertheless, 74.6% of the CRAB isolates co-harbored the blaOXA-23 and blaVIM. Only one type of transposons was detected: Tn2008 (79.1%, 53/67). Although 12 distinctive types (A-L) were determined (primarily A type) ST195 was the most prevalent sequence type (ST). ST368, ST210, ST90, ST829, and ST136 were also detected, and all belonged to clonal complex 208 (CC208) and global complex 2 (GC2).@*Conclusion:@#The blaOXA-23 and blaVIM genes contributed to the resistance among CRAB isolates collected in our study. Notably, most of the CRAB strains co-harbored blaOXA-23 and blaVIM genes, as well as Tn2008, which could contribute to clonal dissemination. The prevalence of such organisms may underlie hospital acquired infections.

Conjugative transfer of resistance determinants among human and bovine Streptococcus agalactiae

Streptococcus agalactiae (GBS) is a major source of human perinatal diseases and bovine mastitis. Erythromycin (Ery) and tetracycline (Tet) are usually employed for preventing human and bovine infections although resistance to such agents has become common among GBS strains. Ery and Tet resistance genes are usually carried by conjugative transposons (CTns) belonging to the Tn916 family, but their presence and transferability among GBS strains have not been totally explored. Here we evaluated the presence of Tet resistance genes (tetM and tetO) and CTns among Ery-resistant (Ery-R) and Ery-susceptible (Ery-S) GBS strains isolated from human and bovine sources; and analyzed the ability for transferring resistance determinants between strains from both origins. Tet resistance and int-Tn genes were more common among Ery-R when compared to Ery-S isolates. Conjugative transfer of all resistance genes detected among the GBS strains included in this study (ermA, ermB, mef, tetM and tetO), in frequencies between 1.10-7 and 9.10-7, was possible from bovine donor strains to human recipient strain, but not the other way around. This is, to our knowledge, the first report of in vitro conjugation of Ery and Tet resistance genes among GBS strains recovered from different hosts.

Presencia del elemento genético transportable dTdic1 en Dianthus caryophyllus con flores variegadas y no variegadas / Presence of the transposable genetic element dTdic1 in Dianthus caryophyllus with variegated and no variegated flowers

El objetivo de este trabajo era la búsqueda del EGT (Elemento Genético Transponible) dTdic1 que ha sido asociado con la variegación del color de las flores de clavel y su relación con dos genes que codifican para enzimas involucradas en la biosíntesis de antocianinas, Chalcona isomerasa (CHI) y Dihidroflavonol reductasa (DFR). Su presencia y expresión se evaluó en siete genotipos con flores variegadas (líneas híbridas) y en cuatro genotipos de flores no variegadas (una línea híbrida y tres cultivares comerciales). Un alto número (indefinido) de copias del elemento dTdic1 se detectó en todas las líneas variegadas y no variegadas. En consecuencia, la sola presencia de este EGT no pudo asociarse directamente con la variegación de los pigmentos florales de flores de clavel. Adicionalmente, dTdic1 se encontró interrumpiendo el gen CHI en cuatro genotipos variegados y uno no variegado. No se observó evidencia de inserción de dTdic1 en el gen DFR en ninguno de los genotipos.

The objective of this work was to search for the EGT (Transposable Genetic Element) dTdic1 that has been associated with color variegation of carnation flowers and its relationship with two genes that code for enzymes involved in the synthesis of anthocyanins, Chalcona isomerase (CHI) and Dihidroflavonol reductase (DFR). Its presence and expression was evaluated in seven genotypes of variegated flowers and four no variegated flower genotypes (one hybrid line and three commercial cultivars). A high number of copies (undefined) of copies of the dTdic1 element was detected in variegaated and no variegated lines. Therefore, the main presence of this EGT was not associated directly with variegation of floral pigments. Additionally, dTdic1 was found interrupting the CHI gene in four variegated and one no variegated phenotypes. No evidence was observed of insertion of dTdic1 in the DFR gene in any of the genotypes.

Heat shock protein 90: a capacitor or a mutator.

Heat shock protein 90 (Hsp90) is a molecular chaperone required for folding, maturation and activity of a select set of proteins important for signal transduction and development. The last decade witnessed this chaperone come into the limelight after the observation that Hsp90 inhibition in developing fruit fl ies results in a large phenotypic variation (Rutherford and Lindquist 1998). This has been interpreted to mean that genetic variation existing within a population does not translate into phenotypic variation under normal circumstances due to ‘buffering’ activity of Hsp90. A recent study has questioned this interpretation and it is proposed that Hsp90 may in fact actively suppress the generation of genetic variation rather than or in addition to merely buffering the phenotypic consequences (Specchia et al. 2010). Specifi cally it was found that fruit fl ies with an impaired Hsp90 activity exhibit an enhanced mobilization of transposons in the germ-line leading to an increased mutation rate. When a phenotypically uniform laboratory population was exposed to sub-lethal doses of Hsp90 inhibitor during development, a variety of morphological abnormalities were expressed. This was found to be the case even when Hsp90 loss-of-function alleles were introduced in an otherwise wild-type genetic background. These initial observations made by Susan Lindquist and colleagues in the fruit fl y Drosophila melanogaster were later on extended to be valid in plants, fungi, slime moulds and fi sh (reviewed in Rutherford et al. 2007). The spectrum of morphological traits in fl ies was shown to be strain-background dependent. Moreover, continued phenotypic selection for an abnormal morphology resulted in increased frequency of that morphology over a few generations, and in expression of the trait even when Hsp90 function was restored (Sangster et al. 2004). This indicates an existence of a genetic component to the Hsp90-induced morphological alterations. Taken together, these observations led to the belief that under normal conditions Hsp90 minimizes phenotypic consequences of random mutations arising in a population, thus exhibiting a ‘canalized’ uniform phenotype despite genetic differences. This in turn means that genetic variation can accumulate over long periods within an interbreeding group of organisms with little deleterious fi tness consequences, if the environmental conditions remain constant. However, when such a genetically diverse population is exposed to stress akin to experimental inhibition of Hsp90, the genetic variation could then manifest itself as a phenotypically heterogeneous population. This can serve as a substrate upon which natural selection can act, resulting in propagation of those phenotypic variants which survive the stressful environment. Hsp90 was thus termed as a ‘capacitor’ for morphological evolution with an analogy to electrical capacitors that store charge only to release it when required. This line of thinking was expanded in its scope later by the observation that Hsp90 inhibition causes phenotypic variation even in highly inbred, genetically uniform population of fruit fl ies (Sollars et al. 2003). Thus Hsp90 is thought to buffer genetic as well as heritable epigenetic variation. The Hsp90 capacitor hypothesis brings to the fore and provides a mechanism for Waddington’s observations of genetic assimilation (Waddington 1959). Taking as an example of evolution of callosities in the ostrich footpads, Waddington proposed that cryptic variation, initially unmasked by an environmental agent (e.g. stress), could provide a driving force for new morphological traits. Hsp90 may have been an important mechanism for genetic assimilation during evolution. Central to the Hsp90 capacitor hypothesis is an ill-supported assumption that phenotypic variation observed upon Hsp90 inhibition is due to pre-existing genetic and/or epigenetic variation. A recent study (Specchia et al. 2010) shows that this assumption need not be true. Working with the fruit fly.

Occurrence and abundance of a mariner-like element in freshwater and terrestrial planarians (Platyhelminthes, Tricladida) from southern Brazil

Transposable elements are DNA sequences present in all the large phylogenetic groups, both capable of changing position within the genome and constituting a significant part of eukaryotic genomes. The mariner family of transposons is one of the few which occurs in a wide variety of taxonomic groups, including freshwater planarians. Nevertheless, so far only five planarian species have been reported to carry mariner-like elements (MLEs), although several different species have been investigated. Regarding the number of copies of MLEs, Girardia tigrina is the only planarian species in which this has been evaluated, with an estimation of 8,000 copies of the element per haploid genome. Preliminary results obtained in our laboratory demonstrated that MLE is found in a large number of different species of planarians, including terrestrial. With this in mind, the aim was to evaluate the occurrence and estimate the number of MLE copies in different planarian species collected in south Brazil. Twenty-eight individuals from 15 planarian species were analyzed. By using PCR and the hybridization of nucleic acids, it was found that MLE was present in all the analyzed species, the number of copies being high, probably over 10³ per haploid genome.