Operons and SL2 trans-splicing exist in nematodes outside the genus Caenorhabditis

The genomes of most eukaryotes are composed of genes arranged on the chromosomes without regard to function, with each gene transcribed from a promoter at its 5′ end. However, the genome of the free-living nematode Caenorhabditis elegans contains numerous polycistronic clusters similar to bacterial operons in which the genes are transcribed sequentially from a single promoter at the 5′ end of the cluster. The resulting polycistronic pre-mRNAs are processed into monocistronic mRNAs by conventional 3′ end formation, cleavage, and polyadenylation, accompanied by trans-splicing with a specialized spliced leader (SL), SL2. To determine whether this mode of gene organization and expression, apparently unique among the animals, occurs in other species, we have investigated genes in a distantly related free-living rhabditid nematode in the genus Dolichorhabditis (strain CEW1). We have identified both SL1 and SL2 RNAs in this species. In addition, we have sequenced a Dolichorhabditis genomic region containing a gene cluster with all of the characteristics of the C. elegans operons. We show that the downstream gene is trans-spliced to SL2. We also present evidence that suggests that these two genes are also clustered in the C. elegans and Caenorhabditis briggsae genomes. Thus, it appears that the arrangement of genes in operons pre-dates the divergence of the genus Caenorhabditis from the other genera in the family Rhabditidae, and may be more widespread than is currently appreciated.

Recurrent invasion and extinction of a selfish gene

Homing endonuclease genes show super-Mendelian inheritance, which allows them to spread in populations even when they are of no benefit to the host organism. To test the idea that regular horizontal transmission is necessary for the long-term persistence of these genes, we surveyed 20 species of yeasts for the ω-homing endonuclease gene and associated group I intron. The status of ω could be categorized into three states (functional, nonfunctional, or absent), and status was not clustered on the host phylogeny. Moreover, the phylogeny of ω differed significantly from that of the host, strong evidence of horizontal transmission. Further analyses indicate that horizontal transmission is more common than transposition, and that it occurs preferentially between closely related species. Parsimony analysis and coalescent theory suggest that there have been 15 horizontal transmission events in the ancestry of our yeast species, through simulations indicate that this value is probably an underestimate. Overall, the data support a cyclical model of invasion, degeneration, and loss, followed by reinvasion, and each of these transitions is estimated to occur about once every 2 million years. The data are thus consistent with the idea that frequent horizontal transmission is necessary for the long-term persistence of homing endonuclease genes, and further, that this requirement limits these genes to organisms with easily accessible germ lines. The data also show that mitochondrial DNA sequences are transferred intact between yeast species; if other genes do not show such high levels of horizontal transmission, it would be due to lack of selection, rather than lack of opportunity.

The restriction–modification genes of Escherichia coli K-12 may not be selfish: They do not resist loss and are readily replaced by alleles conferring different specificities

Type II restriction and modification (R-M) genes have been described as selfish because they have been shown to impose selection for the maintenance of the plasmid that encodes them. In our experiments, the type I R-M system EcoKI does not behave in the same way. The genes specifying EcoKI are, however, normally residents of the chromosome and therefore our analyses were extended to monitor the deletion of chromosomal genes rather than loss of plasmid vector. If EcoKI were to behave in the same way as the plasmid-encoded type II R-M systems, the loss of the relevant chromosomal genes by mutation or recombination should lead to cell death because the cell would become deficient in modification enzyme and the bacterial chromosome would be vulnerable to the restriction endonuclease. Our data contradict this prediction; they reveal that functional type I R-M genes in the chromosome are readily replaced by mutant alleles and by alleles encoding a type I R-M system of different specificity. The acquisition of allelic genes conferring a new sequence specificity, but not the loss of the resident genes, is dependent on the product of an unlinked gene, one predicted [Prakash-Cheng, A., Chung, S. S. & Ryu, J. (1993) Mol. Gen. Genet. 241, 491–496] to be relevant to control of expression of the genes that encode EcoKI. Our evidence suggests that not all R-M systems are evolving as “selfish” units; rather, the diversity and distribution of the family of type I enzymes we have investigated require an alternative selective pressure.

An Escherichia coli strain with all chromosomal rRNA operons inactivated: Complete exchange of rRNA genes between bacteria

Current global phylogenies are built predominantly on rRNA sequences. However, an experimental system for studying the evolution of rRNA is not readily available, mainly because the rRNA genes are highly repeated in most experimental organisms. We have constructed an Escherichia coli strain in which all seven chromosomal rRNA operons are inactivated by deletions spanning the 16S and 23S coding regions. A single E. coli rRNA operon carried by a multicopy plasmid supplies 16S and 23S rRNA to the cell. By using this strain we have succeeded in creating microorganisms that contain only a foreign rRNA operon derived from either Salmonella typhimurium or Proteus vulgaris, microorganisms that have diverged from E. coli about 120–350 million years ago. We also were able to replace the E. coli rRNA operon with an E. coli/yeast hybrid one in which the GTPase center of E. coli 23S rRNA had been substituted by the corresponding domain from Saccharomyces cerevisiae. These results suggest that, contrary to common belief, coevolution of rRNA with many other components in the translational machinery may not completely preclude the horizontal transfer of rRNA genes.

Restriction-modification gene complexes as selfish gene entities: Roles of a regulatory system in their establishment, maintenance, and apoptotic mutual exclusion

We have reported some type II restriction-modification (RM) gene complexes on plasmids resist displacement by an incompatible plasmid through postsegregational host killing. Such selfish behavior may have contributed to the spread and maintenance of RM systems. Here we analyze the role of regulatory genes (C), often found linked to RM gene complexes, in their interaction with the host and the other RM gene complexes. We identified the C gene of EcoRV as a positive regulator of restriction. A C mutation eliminated postsegregational killing by EcoRV. The C system has been proposed to allow establishment of RM systems in new hosts by delaying the appearance of restriction activity. Consistent with this proposal, bacteria preexpressing ecoRVC were transformed at a reduced efficiency by plasmids carrying the EcoRV RM gene complex. Cells carrying the BamHI RM gene complex were transformed at a reduced efficiency by a plasmid carrying a PvuII RM gene complex, which shares the same C specificity. The reduction most likely was caused by chromosome cleavage at unmodified PvuII sites by prematurely expressed PvuII restriction enzyme. Therefore, association of the C genes of the same specificity with RM gene complexes of different sequence specificities can confer on a resident RM gene complex the capacity to abort establishment of a second, incoming RM gene complex. This phenomenon, termed “apoptotic mutual exclusion,” is reminiscent of suicidal defense against virus infection programmed by other selfish elements. pvuIIC and bamHIC genes define one incompatibility group of exclusion whereas ecoRVC gene defines another.

Prediction of operons in microbial genomes

Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons. This study describes a computational method to estimate the likelihood that such conserved gene sets form operons. The method was used to analyze 34 bacterial and archaeal genomes, and yielded more than 7600 pairs of genes that are highly likely (P ≥ 0.98) to belong to the same operon. The sensitivity of our method is 30–50% for the Escherichia coli genome. The predicted gene pairs are available from our World Wide Web site http://www.tigr.org/tigr-scripts/operons/operons.cgi.

Genomics of pyrrolnitrin biosynthetic loci: evidence for conservation and whole-operon mobility within Gram-negative bacteria

Pyrrolnitrin (PRN) is a tryptophan-derived secondary metabolite produced by a narrow range of Gram-negative bacteria. The PRN biosynthesis by rhizobacteria presumably has a key role in their life strategies and in the biocontrol of plant diseases. The biosynthetic operon that encodes the pathway that converts tryptophan to PRN is composed of four genes, prnA through D, whose diversity, genomic context and spread over bacterial genomes are poorly understood. Therefore, we launched an endeavour aimed at retrieving, by in vitro and in silico means, diverse bacteria carrying the prnABCD biosynthetic loci in their genomes. Analysis of polymorphisms of the prnD gene sequences revealed a high level of conservation between Burkholderia, Pseudomonas and Serratia spp. derived sequences. Whole-operon- and prnD-based phylogeny resulted in tree topologies that are incongruent with the taxonomic status of the evaluated strains as predicted by 16S rRNA gene phylogeny. The genomic composition of c. 20 kb DNA fragments containg the PRN operon varied in different strains. Highly conserved and distinct transposase-encoding genes surrounding the PRN biosynthetic operons of Burkholderia pseudomallei strains were found. A prnABCD-deprived genomic region in B. pseudomallei strain K96243 contained the same gene composition as, and shared high homology with, the flanking regions of the PRN operon in B. pseudomallei strains 668, 1106a and 1710b. Our results strongly suggest that the PRN biosynthetic operon is mobile. The extent, frequency and promiscuity of this mobility remain to be understood.

Co-occurrence of three types of egg policing in the Norwegian wasp Dolichovespula norwegica

In insect societies, workers often try to challenge the reproductive monopoly of the queen by laying their own eggs. Successful worker reproduction, however, is frequently prevented by queen policing or worker policing, whereby either the mother queen or non-reproductive workers selectively kill worker-laid eggs. Recently, a third mechanism-""selfish"" worker policing-has also been described in which the workers selectively police worker-laid eggs but also lay eggs themselves. Here, we present results from the monogynous wasp Dolichovespula norwegica, which show that all three kinds of policing-queen policing, worker policing and ""selfish"" worker policing-co-occur. The net effect of these three kinds of policing collectively favoured the queen`s reproduction, as within 1 day 44% of the worker-laid eggs versus only 8% of the queen-laid eggs were eaten. Of the worker-laid eggs that were killed by workers, approximately two thirds were eaten by the reproductive workers even though these made up only a small proportion, 8%, of the work force. This means that policing workers obtained both direct fitness benefits as well as indirect (inclusive) fitness. In addition, we show that worker policing was carried out by a limited, specialised set of workers that was estimated to constitute approximately one quarter of the whole colony and of which 66% were non-reproductive.

Microdistribution of juveniles and adults of the mud crab Panopeus americanus (Brachyura, Panopeidae) in a remnant mangrove area in the southwest Atlantic

The distribution and density of a population of the narrowback mud crab Panopeus americanus were evaluated, with emphasis on the different developmental stages (juveniles and adults) and sexes. Specimens were collected in a remnant human-impacted mangrove at Araca on the northern coast of Sao Paulo, Brazil, at two-month intervals from January through July 2006, using 1m x 1m sample plots randomly distributed in the intertidal zone. The population was abundant, with a mean density of 14.3 +/- 9.3 individuals/m(2). Larger individuals were more abundant in the upper and middle intertidal zones, whereas smaller crabs were predominant in the lower intertidal and thus remained submerged longer. Males and juveniles were homogeneously distributed. Females preferred regions farther from the waterline. A clustered distribution pattern suggested gregarious behaviour and settling of juveniles in the vicinity of the adults` habitats, in an adaptive process as a function of tidal rhythms.

Phylogenetic analysis of evolutionary relationships of the planctomycete division of the domain bacteria based on amino acid sequences of elongation factor Tu

Sequences from the tuf gene coding for the elongation factor EF-Tu were amplified and sequenced from the genomic DNA of Pirellula marina and Isosphaera pallida, two species of bacteria within the order Planctomycetales. A near-complete (1140-bp) sequence was obtained from Pi. marina and a partial (759-bp) sequence was obtained for I. pallida. Alignment of the deduced Pi. marina EF-Tu amino acid sequence against reference sequences demonstrated the presence of a unique Il-amino acid sequence motif not present in any other division of the domain Bacteria. Pi. marina shared the highest percentage amino acid sequence identity with I. pallida but showed only a low percentage identity with other members of the domain Bacteria. This is consistent with the concept of the planctomycetes as a unique division of the Bacteria. Neither primary sequence comparison of EF-Tu nor phylogenetic analysis supports any close relationship between planctomycetes and the chlamydiae, which has previously been postulated on the basis of 16S rRNA. Phylogenetic analysis of aligned EF-Tu amino acid sequences performed using distance, maximum-parsimony, and maximum likelihood approaches yielded contradictory results with respect to the position of planctomycetes relative to other bacteria, It is hypothesized that long-branch attraction effects due to unequal evolutionary rates and mutational saturation effects may account for some of the contradictions.

Os gêneros de discurso, cenografia e ethos em discursos da obra O templo e a forca de Luiz Guilherme Santos Neves

A pesquisa busca mostrar como o discurso religioso do gênero sermão, na voz do enunciador Frei Gregório José Maria de Bene, pode influir na estratégia de adesão e convencimento dos escravos da região de Serra, província do Espírito Santo, para a construção da igreja do Queimado. O sermão citado é o recorte fundamental do discurso literário O Templo e a Forca (1999), recriado por Luiz Guilherme Santos Neves, analisado a partir de cena englobante legitimadora. O trabalho insere-se nos estudos da Analise do Discurso (AD) de linha francesa, pelo referencial teórico de Dominique Maingueneau, que nos orientará quanto às cenografias do padre, sua imagem de enunciador, as condições de produção do sermão, ressaltando elementos que interagem no embate, visando à sociedade da época e às questões culturais dos envolvidos na eclosão da revolta. O principal objetivo é examinar as cenas de enunciação e como se constrói o ethos religioso em cada cena e suas variadas funções. É elementar dizer que o religioso se reconstrói a cada momento a partir do comprometimento com as situações de comunicação. Para maior entendi-mento, dizemos que essas diversas reconstruções apresentam nos discursos diferentes encenações desse tão fomentado religioso com suas estratégias de adesão, apresentando-se ora com a imagem daquele que fala em nome de Deus, preza a docilidade da vida do campo à sombra das andirobeiras gigantes onde se pode sentir o silêncio que convida à contemplação e à prece; ora aquele comprometido com seus propósitos interesseiros e pessoais. Fala para não ser entendido, e o que vale é erguer a casa de São José sem poupar a carne e o sangue das mortes que virão. Importa ressaltar que sempre há possibilidade de olhar ingênuo sobre texto religioso, que, conforme Main-gueneau (2010), só é legível relacionado a vasto intertexto que contribuirá para estruturar o discurso. Para enriquecer ainda mais este estudo, afora o gênero sermão usamos recortes que estruturam o discurso de Neves e sinalizam as variadas cenografias e a forma como se constituem enquanto gêneros: Diálogo interior – momentos solitários do frade – Visão do frade e Monólogo; Diálogo Compartilhado – segmenta diálogos entre o enunciador e seus vários co-enunciadores, que estruturam os acontecimentos do discurso; e o gênero exortação, do padre aos escravos. Os recortes são momentos de grandes embates recriados pelo autor, em discurso leve fazendo seu leitor transitar prazerosamente junto ao frade entre as suas variadas imagens nos discursos. Levando o leitor a acreditar tratar-se de cenas relacionadas ao gênero cômico. E talvez o fosse, se não terminasse em revolta.

Performance evaluation of a cooperative reputation system for vehicular delay-tolerant networks

In the last decade, both scientific community and automotive industry enabled communications among vehicles in different kinds of scenarios proposing different vehicular architectures. Vehicular delay-tolerant networks (VDTNs) were proposed as a solution to overcome some of the issues found in other vehicular architectures, namely, in dispersed regions and emergency scenarios. Most of these issues arise from the unique characteristics of vehicular networks. Contrary to delay-tolerant networks (DTNs), VDTNs place the bundle layer under the network layer in order to simplify the layered architecture and enable communications in sparse regions characterized by long propagation delays, high error rates, and short contact durations. However, such characteristics turn contacts very important in order to exchange as much information as possible between nodes at every contact opportunity. One way to accomplish this goal is to enforce cooperation between network nodes. To promote cooperation among nodes, it is important that nodes share their own resources to deliver messages from others. This can be a very difficult task, if selfish nodes affect the performance of cooperative nodes. This paper studies the performance of a cooperative reputation system that detects, identify, and avoid communications with selfish nodes. Two scenarios were considered across all the experiments enforcing three different routing protocols (First Contact, Spray and Wait, and GeoSpray). For both scenarios, it was shown that reputation mechanisms that punish aggressively selfish nodes contribute to increase the overall network performance.

Reciprocity, inequity aversion, and oligopolistic competition

This paper studies how reciprocity and inequity aversion influence the behavior of firms in imperfectly competitive markets. The paper shows that if reciprocal firms compete à la Cournot, then they are able to sustain “collusive” outcomes under a positive reciprocity equilibrium. By contrast, Stackelberg warfare outcomes may emerge under a negative reciprocity equilibrium. The results for inequity aversion are similar. Cournot competition between inequity averse firms can be harmful to consumers if it leads to equilibria where firms feel compassion toward each other. However, in equilibria where inequity averse firms are envious of each other consumers are better off than if firms were selfish. The paper also shows that only under very restrictive conditions does reciprocity or inequity aversion have an impact on Bertrand competition. Finally, the paper shows that non-selfish preferences have a greater impact on equilibrium outcomes in markets with a small number of firms.

Collusion and reciprocity in infinitely repeated games

This paper extends the standard industrial organization models of repeated interaction between firms by incorporating preferences for reciprocity. A reciprocal firm responds to unkind behavior of rivals with unkind actions (destructive reciprocity), while at the same time, it responds to kind behavior of rivals with kind actions (constructive reciprocity). The main finding of the paper is that, for plausible perceptions of fairness, preferences for reciprocity facilitate collusion in infinitely repeated market games, that is, the critical discount rate at wish collusion can be sustained tends to be lower when firms have preferences for reciprocity than when firms are selfish. The paper also finds that the best collusive outcome that can be sustained in the infinitely repeated Cournot game with reciprocal firms is worse for consumers than the best collusive outcome that can be sustained in the infinitely repeated Cournot game with selfish firms.