The maintenance of sex in bacteria is ensured by its potential to reload genes

Why sex is maintained in nature is a fundamental question in biology. Natural genetic transformation (NGT) is a sexual process by which bacteria actively take up exogenous DNA and use it to replace homologous chromosomal sequences. As it has been demonstrated, the role of NGT in repairing deleterious mutations under constant selection is insufficient for its survival, and the lack of other viable explanations have left no alternative except that DNA uptake provides nucleotides for food. Here we develop a novel simulation approach for the long-term dynamics of genome organization (involving the loss and acquisition of genes) in a bacterial species consisting of a large number of spatially distinct populations subject to independently fluctuating ecological conditions. Our results show that in the presence of weak inter-population migration NGT is able to subsist as a mechanism to reload locally lost, intermittently selected genes from the collective gene pool of the species through DNA uptake from migrants. Reloading genes and combining them with those in locally adapted genomes allow individual cells to re-adapt faster to environmental changes. The machinery of transformation survives under a wide range of model parameters readily encompassing real-world biological conditions. These findings imply that the primary role of NGT is not to serve the cell with food, but to provide homologous sequences for restoring genes that have disappeared from or become degraded in the local population.Comment: 16 pages with 3 color figures. Manuscript accepted for publication in Genetics (www.genetics.org

Az autofág gének szerepe az öregedési folyamat szabályozásában a fonálféreg Caenorhabditis elegansban = Coordinated regulation of ageing by autophagy genes in the nematode Caenorhabditis elegans

Meghatároztuk az élesztő autofág gének nematóda ortológjait. Számos C. elegans autofág gén funkcióvesztéses mutáns alléljét izoláltuk és/vagy specifikus RNS intereferencia klónját állítottuk elő. Autofágia defektív C. elegans törzseket genetikailag jellemeztük. Három C. elegans autofág gén esetében transzlációs fúziós riporter konstrukciót hoztunk létre és jellemeztük a gének expressziós mintázatát. Megállapítottuk, hogy az autofágia deficiens nematódák rövidebb ideig élnek a vad típusnál. Ezek az állatok gyorsabban halmoztak fel öregedési pigmenteket és hamarabb váltak paralizálttá, mint a vad típusú kontroll állatok. Autofágia hiányában tehát az állatok gyorsabban öregednek. Ezzel összhangban az inzulin/IGF-1 és TOR kináz útvonal deficiens mutáns fonalférgek, a csökkent mitokondriális respirációjú mutánsok és a kalorikusan csökkent tápanyagfelvételű mutáns állatok hosszú élettartamát az autofágia blokkolása szuppresszálta (az autofág mutációk episztatikusan hatottak). Az élethosszt szabályozó genetikai útvonalak tehát az autofág génkaszkádon konvergálódnak (az autofágia az öregedési folyamat központi szabályozó mechanizmusa). Kimutattuk, hogy az autofág gének és az apoptotikus génkaszkád redundánsan hatnak az embrionális fejlődés szabályozásában. Végül meghatároztunk egy myotubularin-szerű foszfatázt, amely negatívan szabályozza az autofágiát: ennek gátlásával az autofág folyamatot hiperaktiváltuk, és ez növelte az élettartamot és neuroprotektív hatású volt. | We identified the nematode orthologs of yeast autophagy genes. We then isolated loss-of-function mutations in some of these worm autophagy genes or generated their specific RNA interference clones. We performed a genetic analysis of autophagy deficient nematode strains. In the case of three autophagy genes, we also generated translational fusion reporter constructs to determine their developmental expression pattern. Nematodes defective for autophagy live significantly shorter than the wild-type. These mutants accumulate age pigments (lipofuscin) faster and become paralyzed earlier than normal animals. Thus, autophagy deficient nematodes are progeric as they exhibit an accelerated rate at which the cells and tissues age. Consistently, autophagy genes are required for lifespan extension in insulin/IGF-1 and TOR signaling mutants, in nematodes with decreased mitochondrial respiration and in calorically restricted worms; the corresponding double mutants are short-lived (autophagy mutations are epistatic to longevity mutations). Together, we can conclude that autophagy act as a central regulatory mechanism of animal aging. We also revealed that autophagy genes function redundantly with the apoptotic gene cascade to control embryonic development. Finally, we determined a myotubularin-like phosphatase that is able to downregulate the autophagic process. Inhibition of this phosphatase was capable of extending lifespan and protecting against neuronal damage

The metastasis suppressor Nm23 as a modulator of Ras/ERK signaling.

NM23-H1 (also known as NME1) was the first identified metastasis suppressor, which displays a nucleoside diphosphate kinase (NDPK) and histidine protein kinase activity. NDPKs are linked to many processes, such as cell migration, proliferation, differentiation, but the exact mechanism whereby NM23-H1 inhibits the metastatic potential of cancer cells remains elusive. However, some recent data suggest that NM23-H1 may exert its anti-metastatic effect by blocking Ras/ERK signaling. In mammalian cell lines NDPK-mediated attenuation of Ras/ERK signaling occurs through phosphorylation (thus inactivation) of KSR (kinase suppressor of Ras) scaffolds. In this review I summarize our knowledge about KSR's function and its regulation in mammals and in C. elegans. Genetic studies in the nematode contributed substantially to our understanding of the function and regulation of the Ras pathway (i.e. KSR's discovery is also linked to the nematode). Components of the RTK/Ras/ERK pathway seem to be highly conserved between mammals and worms. NDK-1, the worm homolog of NM23-H1 affects Ras/MAPK signaling at the level of KSRs, and a functional interaction between NDK-1/NDPK and KSRs was first demonstrated in the worm in vivo. However, NDK-1 is a factor, which is necessary for proper MAPK activation, thus it activates rather than suppresses Ras/MAPK signaling in the worm. The contradiction between results in mammalian cell lines and in the worm regarding NDPKs' effect exerted on the outcome of Ras signaling might be resolved, if we better understand the function, structure and regulation of KSR scaffolds

The C. elegans Hox gene ceh-13 regulates cell migration and fusion in a non-colinear way. Implications for the early evolution of Hox clusters

Background: Hox genes play a central role in axial patterning during animal development. They are clustered in the genome and specify cell fate in sequential domains along the anteroposterior (A-P) body axis in a conserved order that is co-linear with their relative genomic position. In the soil worm Caenorhabditis elegans, this striking rule of co-linearity is broken by the anterior Hox gene ceh-13, which is located between the two middle Hox paralogs, lin-39 and mab-5, within the loosely organized nematode Hox cluster. Despite its evolutionary and developmental significance, the functional consequence of this unusual genomic organization remains unresolved.Results: In this study we have investigated the role of ceh-13 in different developmental processes, and found that its expression and function are not restricted to the anterior body part. We show that ceh-13 affects cell migration and fusion as well as tissue patterning in the middle and posterior body regions too. These data reveal novel roles for ceh-13 in developmental processes known to be under the control of middle Hox paralogs. Consistently, enhanced activity of lin-39 and mab-5 can suppress developmental arrest and morphologic malformation in ceh-13 deficient animals.Conclusion: Our findings presented here show that, unlike other Hox genes in C. elegans which display region-specific accumulation and function along the A-P axis, the expression and functional domain of the anterior Hox paralog ceh-13 extends beyond the anterior region of the worm. Furthermore, ceh-13 and the middle Hox paralogs share several developmental functions. Together, these results suggest the emergence of the middle-group Hox genes from a ceh-13-like primordial Hox ancestor

Heat shock factor-1 intertwines insulin/IGF-1, TGF-beta and cGMP signaling to control development and aging.

ABSTRACT: BACKGROUND: Temperature affects virtually all cellular processes. A quick increase in temperature challenges the cells to undergo a heat shock response to maintain cellular homeostasis. Heat shock factor-1 (HSF-1) functions as a major player in this response as it activates the transcription of genes coding for molecular chaperones (also called heat shock proteins) that maintain structural integrity of proteins. However, the mechanisms by which HSF-1 adjusts fundamental cellular processes such as growth, proliferation, differentiation and aging to the ambient temperature remain largely unknown. RESULTS: We demonstrate here that in Caenorhabditis elegans HSF-1 represses the expression of daf-7 encoding a TGF-beta (transforming growth factor-beta) ligand, to induce young larvae to enter the dauer stage, a developmentally arrested, non-feeding, highly stress-resistant, long-lived larval form triggered by crowding and starvation. Under favorable conditions, HSF-1 is inhibited by crowding pheromone-sensitive guanylate cyclase/cGMP (cyclic guanosine monophosphate) and systemic nutrient-sensing insulin/IGF-1 (insulin-like growth factor-1) signaling; loss of HSF-1 activity allows DAF-7 to promote reproductive growth. Thus, HSF-1 interconnects the insulin/IGF-1, TGF-beta and cGMP neuroendocrine systems to control development and longevity in response to diverse environmental stimuli. Furthermore, HSF-1 upregulates another TGF-beta pathway-interacting gene, daf-9/cytochrome P450, thereby fine-tuning the decision between normal growth and dauer formation. CONCLUSION: Together, these results provide mechanistic insight into how temperature, nutrient availability and population density coordinately influence development, lifespan, behavior and stress response through HSF-1

Autophagy in zebrafish

From a hitherto underappreciated phenomenon, autophagy has become one of the most intensively studied cellular processes in recent years. Its role in cellular homeostasis, development and disease is supported by a fast growing body of evidence. Surprisingly, only a small fraction of new observations regarding the physiological functions of cellular "self-digestion" comes from zebrafish, one of the most popular vertebrate model organisms. Here we review the existing information about autophagy reporter lines, genetic knock-down assays and small molecular reagents that have been tested in this system. As we argue, some of these tools have to be used carefully due to possible pleiotropic effects. However, when applied rigorously, in combination with novel mutant strains and genome editing techniques, they could also transform zebrafish into an important animal model of autophagy research

The genome loading model for the origin and maintenance of sex in eukaryotes

Understanding why sexual reproduction—which involves syngamy (union of gametes) and meiosis—emerged and how it has subsisted for millions of years remains a fundamental problem in biology. Considered as the essence of sex, meiotic recombination is initiated by a DNA double-strand break (DSB) that forms on one of the pairing homologous chromosomes. This DNA lesion is subsequently repaired by gene conversion, the non-reciprocal transfer of genetic information from the intact homolog. A major issue is which of the pairing homologs undergoes DSB formation. Accumulating evidence shows that chromosomal sites where the pairing homologs locally differ in size, i.e., are heterozygous for an insertion or deletion, often display disparity in gene conversion. Biased conversion tends to duplicate insertions and lose deletions. This suggests that DSB is preferentially formed on the “shorter” homologous region, which thereby acts as the recipient for DNA transfer. Thus, sex primarily functions as a genome (re)loading mechanism. It ensures the restoration of formerly lost DNA sequences (deletions) and allows the efficient copying and, mainly in eukaryotes, subsequent spreading of newly emerged sequences (insertions) arising initially in an individual genome, even if they confer no advantage to the host. In this way, sex simultaneously repairs deletions and increases genetic variability underlying adaptation. The model explains a remarkable increase in DNA content during the evolution of eukaryotic genomes

PHYTOCHEMICAL SCREENING AND EVALUATION OF IN VITRO ANTIOXIDANT POTENTIAL OF IMMATURE PALMYRA PALM (BORASSUS FLABELLIFER LINN.) FRUITS

Objective: The present study was aimed to evaluate the in vitro antioxidant properties of immature Palmyra palm fruits which have been traditionally used for the treatment of diabetes. The qualitative phytochemical screening and quantitative estimation of total phenolic and flavonoids contents in the ethanolic extract were performed to substantiate the antioxidant and medicinal claims.Methods: Immature palmyra palm fruits were collected, authenticated, dried and powdered in an electrical grinder. The powdered fruits were delipidated in petroleum ether and soxhilation using ethanol to extract the active ingredients. Qualitative phytochemical screening, total phenolic and flavonoid contents were carried out by established methods. The in vitro antioxidant potentials were performed by diphenyl-2-picrylhydrazyl, azino-bis(3-ethylbenzothiazoline-6-sulphonic acid, nitric oxide and superoxide anion scavenging assays.Results: The phytochemical screening showed the presence of alkaloids, flavonoids, glycosides, saponins, tannins, phytosterols, triterpenoids and phenols in the immature palmyra palm fruits extract. The total phenolic and flavonoid contents in the fruits extract was found to be 104.00±0.02 μg gallic acid equivalents/100 mg of fruits extract and 98.45±0.03 μg quercetin equivalents/100 mg, respectively. The percentage inhibition of DPPH radicals range from 35 to 70% at a concentration ranges from 200-1000μg/ml. Similarly, the percentage of inhibition of ABTS radicals was found to be in the range of 40 to 75.5%. The nitric oxide scavenging activity of the fruits extract ranges from 45 to 76% whereas the superoxide radical scavenging activity ranges from 43 to 83%.Conclusion: The observed significant free radical scavenging activity along with increased total phenolic as well as flavonoid contents suggest that the immature fruits may be considered as a potential source for the identification of pharmacologically active phytochemicals capable of controlling oxidative stress

Az autofagocitózis transzkripcionális szabályozása C. elegansban = Transcriptional control of autophagy in C. elegans

C. elegansban genetikai és farmakológiai hatások masszív sejtpusztulást váltanak ki mind apoptotikus, mind autofág jellegzetességekkel. Ezek redundánsan vannak jelen és biztosítják a normális fejlődést. A CES-2-szerű leucin-zipper (bZip) transzkripciós faktor, az ATF-2, az apoptotikus sejthalál központi útvonalának upstream modulátora direkt módon regulálja legalább két autofág gén (bec-1/ATG6 és lgg-1/ATG8) expresszióját. A két sejthalál mechanizmusnak vannak közös transzkripciós elemei. Azonosítottunk négy új metazoa specifikus autofágia gént. Az epg-2,-3,-4, és-5 genetikai analízise felderítette, hogy ezek az autofág útvonal diszkrét genetikai lépéseit jelentik. Az epg-2 egy coiled-coil proteint kódol amely a specifikus kargo felismerésben szerepel. Az EPG-3/VMP1, EPG-4/EI24, és az EPG-5/mEPG5 emlős homológjai eszenciálisak az éhezési autofágiához. A VMP1 az autofagoszóma képződést szabályozza az omegaszómák élettartama révén. Az epg-6 egy eszenciális autofágia gén amely egy PtdIns(3)P-kötő WD-40 repeat proteint kódol. Az EPG-6 direkt módon interakcióba lép az ATG-2-vel. Az epg-6 és az atg-2 regulálja az omegasomák hozzájárulását az autofagoszóma képződéshez. Lf mutációik korai autofág struktúrák felhalmozódásához vezetnek. Egy másik WD40 repeat PtdIns(3)P effektor, az ATG-18, eltérő szerepet játszik az autofagoszóma képződésében. Az Unc-51/Atg-1 komplexum, az EPG-8/Atg14, és a lipidált LGG-1 protein aggregátumokhoz való kötődése szükséges az omegaszóma képződéshez. | We have shown in C. elegans, that various genetic and pharmacologic interventions trigger massive cell death response that has both autophagic and apoptotic features. The two degradation processes are also redundantly required for normal development and viability in this organism. Furthermore, the CES-2-like basic region leucine-zipper (bZip) transcription factor ATF-2, an upstream modulator of the core apoptotic cell death pathway, is able to directly regulate the expression of at least two key autophagy-related genes, bec-1/ATG6 and lgg-1/ATG8. Thus, the two cell death mechanisms share a common method of transcriptional regulation. We identified four metazoan-specific autophagy genes, named epg-2, -3, -4, and -5. Genetic analysis revealed that epg-2, -3, -4, and -5 define discrete genetic steps of the autophagy pathway. epg-2 encodes a coiled-coil protein that functions in specific autophagic cargo recognition. Mammalian homologs of EPG-3/VMP1, EPG-4/EI24, and EPG-5/mEPG5 are essential for starvation-induced autophagy. VMP1 regulates autophagosome formation by controlling the duration of omegasomes. C. elegans epg-6 encodes a WD40 repeat-containing protein with PtdIns(3)P-binding activity. EPG-6 directly interacts with ATG-2. epg-6 and atg-2 regulate progression of omegasomes to autophagosomes, and their loss of function causes accumulation of enlarged early autophagic structures