Main features of DNA-based immunization vectors

DNA-based immunization has initiated a new era of vaccine research. One of the main goals of gene vaccine development is the control of the levels of expression in vivo for efficient immunization. Modifying the vector to modulate expression or immunogenicity is of critical importance for the improvement of DNA vaccines. The most frequently used vectors for genetic immunization are plasmids. In this article, we review some of the main elements relevant to their design such as strong promoter/enhancer region, introns, genes encoding antigens of interest from the pathogen (how to choose and modify them), polyadenylation termination sequence, origin of replication for plasmid production in Escherichia coli, antibiotic resistance gene as selectable marker, convenient cloning sites, and the presence of immunostimulatory sequences (ISS) that can be added to the plasmid to enhance adjuvanticity and to activate the immune system. In this review, the specific modifications that can increase overall expression as well as the potential of DNA-based vaccination are also discussed.

Screening for mutations in human alpha-globin genes by nonradioactive single-strand conformation polymorphism

Point mutations and small insertions or deletions in the human alpha-globin genes may produce alpha-chain structural variants and alpha-thalassemia. Mutations can be detected either by direct DNA sequencing or by screening methods, which select the mutated exon for sequencing. Although small (about 1 kb, 3 exons and 2 introns), the alpha-globin genes are duplicate (alpha2 and alpha1) and highy G-C rich, which makes them difficult to denature, reducing sequencing efficiency and causing frequent artifacts. We modified some conditions for PCR and electrophoresis in order to detect mutations in these genes employing nonradioactive single-strand conformation polymorphism (SSCP). Primers previously described by other authors for radioactive SSCP and phast-SSCP plus denaturing gradient gel electrophoresis were here combined and the resultant fragments (6 new besides 6 original per alpha-gene) submitted to silver staining SSCP. Nine structural and one thalassemic mutations were tested, under different conditions including two electrophoretic apparatus (PhastSystem™ and GenePhor™, Amersham Biosciences), different polyacrylamide gel concentrations, run temperatures and denaturing agents, and entire and restriction enzyme cut fragments. One hundred percent of sensitivity was achieved with four of the new fragments formed, using the PhastSystem™ and 20% gels at 15ºC, without the need of restriction enzymes. This nonradioactive PCR-SSCP approach showed to be simple, rapid and sensitive, reducing the costs involved in frequent sequencing repetitions and increasing the reliability of the results. It can be especially useful for laboratories which do not have an automated sequencer.

Primary structure and expression studies of the dihydrofolate reductase gene (DFRI) of Saccharomyces cerevisiae

The nucleotide sequence of a genomic DNA fragment thought previously to contain the dihydrofolate reductase gene (DFR1) of Saccharomyces cerevisiae by genetic criteria was determined. This DNA fragment of 1784' basepairs contains a large open reading frame from position 800 to 1432, which encodes a enzyme with a predicted molecular weight of 24,229.8 Daltons. Analysis of the amino acid sequence of this protein revealed that the yeast polypep·tide contained 211 amino acids, compared to the 186 residues commonly found in the polypeptides of other eukaryotes. The difference in size of the gene product can be attributed mainly to an insert in the yeast gene. Within this region, several consensus sequences required for processing of yeast nuclear and class II mitochondrial introns were identified, but appear not sufficient for the RNA splicing. The primary structure of the yeast DHFR protein has considerable sequence homology with analogous polypeptides from other organisms, especially in the consensus residues involved in cofactor and/or inhibitor binding. Analysis of the nucleotide sequence also revealed the presence of a number of canonical sequences identified in yeast as having some function in the regulation of gene expression. These include UAS elements (TGACTC) required for tIle amino acid general control response, and "TATA H boxes as well as several consensus sequences thought to be required for transcriptional termination and polyadenylation. Analysis of the codon usage of the yeast DFRl coding region revealed a codon bias index of 0.0083. this valve very close to zero suggestes 3 that the gene is expressed at a relatively low level under normal physiological conditions. The information concerning the organization of the DFRl were used to construct a variety of fusions of its 5' regulatory region with the coding region of the lacZ gene of E. coli. Some of such fused genes encoded a fusion product that expressed in E.coli and/or in yeast under the control of the 5' regulatory elements of the DFR1. Further studies with these fusion constructions revealed that the beta-galactosidase activity encoded on multicopy plasmids was stimulated transiently by prior exposure of yeast host cells to UV light. This suggests that the yeast PFRl gene is indu.ced by UV light and nlay in1ply a novel function of DHFR protein in the cellular responses to DNA damage. Another novel f~ature of yeast DHFR was revealed during preliminary studies of a diploid strain containing a heterozygous DFRl null allele. The strain was constructed by insertion of a URA3 gene within the coding region of DFR1. Sporulation of this diploid revealed that meiotic products segregated 2:0 for uracil prototrophy when spore clones were germinated on medium supplemented with 5-formyltetrahydrofolate (folinic acid). This finding suggests that, in addition to its catalytic activity, the DFRl gene product nlay play some role in the anabolisln of folinic acid. Alternatively, this result may indicate that Ura+ haploid segregants were inviable and suggest that the enzyme has an essential cellular function in this species.

Étude du polymorphisme intra- et inter-spécifique du gène β-tubuline chez des espèces de champignons mycorhiziens à arbuscules en vue de développer des marqueurs moléculaires

Les champignons mycorhiziens à arbuscules (CMA), classés dans le phylum Glomeromycota, ne peuvent pas être facilement identifiés par la morphologie de leurs spores et leurs mycélia à l'intérieur ou à l'extérieur des racines de leurs hôtes. Ce problème fondamental d'identification rend l'étude de leur diversité, en particulier dans leur habitat naturel (sol et racine) extrêmement difficile. Les gènes ribosomaux ont été largement utilisés pour développer des amorces spécifiques et en inférer des arbres phylogénétiques. Cependant, ces gènes sont très polymorphes et existent en plusieurs copies dans le génome des CMA, ce qui complique l’interprétation des résultats. Dans notre étude, nous avons étudié le polymorphisme intra- et inter-spécifique du gène β-tubuline, présent en faible nombre de copies dans le génome des CMA, afin d’obtenir de nouvelles séquences nucléotidiques pour développer des marqueurs moléculaires. Les gènes β-tubuline amplifiés à partir de l'ADN génomique de cinq espèces du genre Glomus ont été clonés et séquencés. L’analyse des séquences indique un polymorphisme intraspécifique chez trois espèces de CMA. Deux séquences paralogues très variables ont été nouvellement identifiées chez les G. aggregatum, G. fasciculatum et G. cerebriforme. Aucun polymorphisme n’a été détecté chez les G. clarum et G. etunicatum. Toutes les séquences montrent la présence de deux introns hautement variables. La majorité des substitutions ont été localisées dans les exons et sont synonymes à 90%. La conservation des acides aminés suggère un niveau élevé de sélection négative sur le gène β-tubuline et nous permet de confirmer que les CMA représentent un ancien groupe fongique (400 million d’années). L’analyse phylogénétique, réalisée avec vingt et une séquences nucléotidiques du gène β-tubuline, a révélé que les séquences des Glomaceae forment un groupe monophylétique bien supporté, avec les Acaulosporaceae et Gigasporaceae comme groupe frère. Les séquences paralogues nouvellement identifiées chez les G. aggregatum et G. fasciculatum n'ont pas été monophylétiques au sein de chaque espèce. Les oligonucléotides ont été choisis sur la base des régions variables et conservées du gène β-tubuline. Le test PCR des amorces β-Tub.cerb.F/ β-Tub.cerb.R a révélé des bandes spécifiques de 401 pb pour les séquences paralogues du G. cerebriforme. Deux paires d’amorces ont été développées afin d’identifier les séquences du groupe nommé Tub.1. Les tests PCR nous ont permis d’identifier certaines séquences du groupe Tub.1. Une paire d’amorce β-Tub.2.F/ β-Tub.2.R nous a permis d’identifier certaines séquences paralogues du groupe nommé Tub.2. L’analyse d’autres gènes combinée à celle du gène β-tubuline permettra le développement de marqueurs moléculaires plus spécifiques pour l’identification de CMA.

Études génétiques moléculaires du gène de la polarité planaire SCRIBBLE1 chez les anomalies du tube neural

Les anomalies du tube neural (ATN), incluant l'anencéphalie et le spina-bifida, représentent un groupe de malformations congénitales très fréquentes chez l'homme. Ces anomalies sont causées par un défaut partiel ou complet de la fermeture du tube neurale au cours de l'embryogenèse. Les ATN ont une étiologie complexe et multifactorielle impliquant des facteurs environnementaux et génétiques. La voie de signalisation non-canonique du Frizzled (Fz)/Dishevelled (Dvl) contrôle la polarité cellulaire planaire (PCP) et le processus morphogénétique appelé l’extension convergente qui est essentiel pour la gastrulation et la fermeture du tube neural. Très important, des mutations des gènes de cette voie étaient fortement associées aux ATN chez la souris et l’humain. Scribble est un gène de la voie PCP qui cause une sévère ATN chez la souris Circletail. Notre étude vise à analyser le rôle de SCRIBBLE1 dans les ATN humains par des analyses de séquence de son cadre de lecture et ses jonctions exon-introns. Notre étude comporte 396 patients recrutés au Centre Spina Bifida de l’hôpital Gaslini en Gènes, Italie et 83 patients recrutés au Centre Spina Bifida de l’hôpital Sainte Justine. Les patients sont affectés par plusieurs formes d’ATN. Nous avons identifié neuf mutations rares et non synonymes chez 10 patients, p.Asp93Ala (c. 435G>A), p.Gly145Arg (c. 278A>C), p.Gly263Ser (c. 786C>A), p.Gly469Ser (c. 1405G>A), p.Pro649His (c. 1946C>A), p.Gln808His (c. 2424G>T), p.Val1066Met (c. 3196G>A), p.Arg1150Gln (c. 3480G>A) et p.Thr1422Met (c. 4266C>T). Cinque mutations, p.Gly263Ser, p.Pro649His, p.Gln808His, p.Arg1150Gln, p.Thr1422Met, étaient absentes dans les contrôles analysés et prédites d’être pathogéniques in silico. Cette étude montre que des mutations rares dans SCRIB1 pourraient augmenter le risque des ATN dans une fraction des patients. L’identification des gènes prédisposant aux ATN nous aidera à mieux comprendre les mécanismes pathogéniques impliqués dans ces maladies.

La dynamique chromatinienne induite par le pic de LH dans les cellules de granulosa chez la souris

La régulation transcriptionnelle des gènes est un processus indispensable sans lequel la diversité phénotypique des cellules ainsi que l’adaptation à leur environnement serait inexistant. L’identification des éléments de régulation dans le génome est d’une importance capitale afin de comprendre les mécanismes gouvernant l’expression des gènes spécifiques à un type cellulaire donné. Ainsi, suite au pic de LH, le follicule ovarien entre dans un programme intensif de différentiation cellulaire, orchestré par des modifications majeures du profile transcriptionnel des cellules de granulosa, déclenchant ultimement l’ovulation et la lutéinisation, processus indispensables à la fertilité femelle. L’hypothèse supportée par cette étude stipule qu’une réorganisation de la structure chromatinienne survient aux régions régulatrices d’une panoplie de gènes dans les heures suivant le pic de LH et qu’en isolant et identifiant ces régions, il serait possible de retrouver des éléments essentiels aux processus d’ovulation et de lutéinisation. Ainsi, en utilisant un protocole standard de superovulation chez la souris, les éléments de régulation se modifiant 4h suivant l’administration de hCG ont été isolés et identifiés dans les cellules de granulosa en utilisant la méthode FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) combinée à un séquençage haut débit. Cette étude a démontré que suite au stimulus ovulatoire, les cellules de granulosa subissent une reprogrammation majeure des éléments de régulation, qui est corrélée avec une modification drastique de leurs fonctions biologiques. De plus, cette étude a mis en évidence une association majoritaire des éléments de régulation à des régions intergéniques distales et à des introns, indiquant que ces régions ont une importance capitale dans la régulation transcriptionnelle dans les cellules de granulosa. Cette étude a également permis d’identifier une panoplie de régulateurs transcriptionnels reconnus pour être essentiels à la fonction ovarienne, ainsi que leur sites de liaison dans le génome, démontrant que la méthode FAIRE est une méthode assez puissante pour permettre la prédiction d’événements moléculaires précis ayant un sens physiologique réel.

Molekulare Studien zur Evolution der Myrmekophytie in der Gattung Macaranga (Euphorbiaceae)

Im Rahmen der vorliegenden Arbeit wurde eine detaillierte phylogenetische Analyse der Ameisenpflanzen aus der Gattung Macaranga (Euphorbiaceae) und ihres verwandtschaftlichen Umfelds mit Hilfe von AFLP-Fingerprinting („amplified fragment length polymorphisms“) sowie vergleichender Analyse von mehreren nichtkodierenden Chloroplasten-DNA-Loci vorgenommen. Anhand dieser Untersuchungen sollten im Wesentlichen die folgenden Fragen geklärt werden: (1) Wie stellen sich die Verwandtschaftsverhältnisse zwischen den myrmekophytischen Macaranga-Sektionen Pachystemon, Winklerianae und Pruinosae dar? (2) Wie sind die einzelnen Arten dieser Sektionen miteinander verwandt? (3) Wie oft ist die Lebensweise ”Myrmekophytie” unabhängig voneinander entstanden? Gibt es Hinweise auf Reversionen? (4) Wo liegt genealogisch und auch geographisch der Ursprung der Symbiose zwischen den myrmekophytischen Macaranga-Arten und ihren Partnerameisen? (5) Welche Bedeutung spielen koevolutive Entwicklungen für das Macaranga-Crematogaster-Symbiosesystem? Ist Myrmekophytie im Sinne einer Schlüsselinnovation (Givnish, 1997) als Stimulus für eine adaptive Radiation zu betrachten? (1) Für die AFLP-Analyse wurden 108 Proben aus 43 Macaranga-Arten und 5 unbeschriebenen Morphospezies in die phylogenetische Untersuchung einbezogen. Auf der Basis von 426 Merkmalen wurden Phänogramme sowie Kladogramme rekonstruiert. Zur statistischen Absicherung wurden Bootstrap-Analysen durchgeführt und im Falle der Kladogramme darüber hinaus der „consistency“-Index bestimmt. Die AFLP-Datensätze wurden zusätzlich einer Hauptkomponentenanalyse unterzogen. Mit Hilfe der verschiedenen Untersuchungsmethoden konnten weitgehend übereinstimmende Gruppierungen bzw. evolutive Linien identifiziert werden. Die Sektionen Pachystemon und Pruinosae bilden eine jeweils gut gestützte monophyletische Gruppe. Beide sind vermutlich Schwestergruppen und damit gleich alt. Für die Monophylie der nur aus zwei Arten bestehenden Sektion Winklerianae ergab sich keine Unterstützung. Die Arten der Sektion Pruinosae sind im AFLP-Baum gut aufgelöst. Die nicht myrmekophytische M. gigantea sitzt dabei an der Basis und ist Schwestergruppe zu den myrmekophytischen Arten. Innerhalb der Sektion Pachystemon wurden mit Hilfe der AFLP-Analyse vier gut gestützte Gruppen identifiziert. Für die puncticulata-Gruppe konnte hier erstmals auf molekularer Ebene eine Zugehörigkeit zur Sekt. Pachystemon nachgewiesen werden. Der von Davies (2001) vorgenommene Ausschluss von M. recurvata aus der Sekt. Pachystemon konnte bestätigt werden. Die Verwandtschaftsbeziehungen einzelner Arten zueinander sind in den AFLP-Bäumen nicht aufgelöst. (2) Für die vergleichende Chloroplasten-Sequenzierung wurden nach Maßgabe der Sequenzvariabilität in Testsequenzierungen die Bereiche atpB-rbcL und psbI-trnS für die phylogenetische Untersuchung ausgewählt. Für die Chloroplasten-Phylogenie wurden für jeden Locus mehr als 100 Sequenzen analysiert. Neben 29 Pachystemon-Arten inkl. vier unbekannter Morphospezies, acht Pruinosae-Arten inkl. eines möglichen Hybriden und den beiden Arten der Sekt. Winklerianae wurden 22 weitere Macaranga- und 10 Mallotus-Arten in die Untersuchung einbezogen. Zwischen den südostasiatischen Arten bestanden nur geringe Sequenzunterschiede. Maximum-Parsimonie-Kladogramme wurden rekonstruiert und die Sequenzen der beiden Loci wurden sowohl einzeln, als auch kombiniert ausgewertet. Indels wurden kodiert und als separate Merkmalsmatrix an die Sequenzdaten angehangen. Innerhalb von Macaranga konnten nur wenige abgesicherte Gruppen identifiziert werden. Deutlich war die Zusammengehörigkeit der afrikanischen Arten und ihr Entstehung aus den südostasiatischen Arten. Die von Davies (2001) der Sektion Pruinosae zugeordnete M. siamensis steht deutlich außerhalb dieser Sektion. Die Arten der Sektionen Pruinosae, Pachystemon und Winklerianae bilden keine statistisch gesicherten monophyletischen Gruppen. Während der Pilotstudien stellte sich heraus, dass die Chloroplastensequenzen nahe verwandter Arten der Sektion Pachystemon weniger nach den Artgrenzen, sondern vielmehr nach geographischen Kriterien gruppierten. (3) Es wurde daher zusätzlich eine phylogeographische Analyse der Chloroplasten-Sequenzen auf der Basis eines Parsimonie-Netzwerks durchgeführt. Neben dem atpB-rbcL-Spacer und einer Teilsequenze des psbI-trnS-Locus (ccmp2) wurde dafür zusätzlich der ccmp6-Locus (ein Abschnitt des ycf3-Introns) sequenziert. Die phylogeographische Untersuchung wurde mit 144 Proben aus 41 Macaranga-Arten durchgeführt. Darin enthalten waren 29 Arten (inkl. vier Morphospezies) mit 112 Proben der Sektion Pachystemon, sieben 7 Arten (inkl. eines potentiellen Hybriden) mit 22 Proben der Sekt. Pruinosae und zwei Arten mit 5 Proben der Sekt. Winklerianae. Das voll aufgelöste statistische Parsimonie-Netzwerk umfasste 88 Haplotypen. Die Sektionen Pachystemon und Pruinosae bilden jeweils eine monophyletische Gruppe. Das geographische Arrangement der Haplotypen unabhängig von der Artzugehörigkeit könnte durch Introgression und/oder „lineage sorting“ bedingt sein. Mit Hilfe der im Rahmen dieser Arbeit gewonnenen Ergebnisse kann man davon ausgehen, dass eine enge Ameisen-Pflanzen-Symbiose innerhalb der Gattung Macaranga mindestens drei-, möglicherweise viermal unabhängig voneinander entstanden ist Eine Reversion hat mindestens einmal, möglicherweise häufiger in der bancana-Gruppe stattgefunden. Ob sich die Symbiose dabei in Westmalaysia oder in Borneo entwickelt hat, kann man nicht sicher sagen; Ob und inwieweit die große Artenzahl in der bancana-Gruppe als eine Folge der Myrmekophytie anzusehen ist, bleibt zunächst offen. Wesentliche Teile der vorliegenden Arbeit liegen bereits in publizierter Form vor (AFLP-Analyse: Bänfer et al. 2004; Chloroplasten-Analyse: Vogel et al. 2003; Bänfer et al. 2006).

Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli

Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs) are non-coding RNAs whose main function in eukaryotes is to guide the modification of nucleotides in ribosomal and spliceosomal small nuclear RNAs, respectively. Full-length sequences of Arabidopsis snoRNAs and scaRNAs have been obtained from cDNA libraries of capped and uncapped small RNAs using RNA from isolated nucleoli from Arabidopsis cell cultures. We have identified 31 novel snoRNA genes (9 box C/D and 22 box H/ACA) and 15 new variants of previously described snoRNAs. Three related capped snoRNAs with a distinct gene organization and structure were identified as orthologues of animal U13snoRNAs. In addition, eight of the novel genes had no complementarity to rRNAs or snRNAs and are therefore putative orphan snoRNAs potentially reflecting wider functions for these RNAs. The nucleolar localization of a number of the snoRNAs and the localization to nuclear bodies of two putative scaRNAs was confirmed by in situ hybridization. The majority of the novel snoRNA genes were found in new gene clusters or as part of previously described clusters. These results expand the repertoire of Arabidopsis snoRNAs to 188 snoRNA genes with 294 gene variants.

Phylogenetic utility of more axillary growth (MAX4 ) - like genes: a case study in Digitalis / Isoplexis (Plantaginaceae)

We present the first assessment of phylogenetic utility of a potential novel low-copy nuclear gene region in flowering plants. A fragment of the MORE AXILLARY GROWTH 4 gene (MAX4, also known as RAMOSUS1 and DECREASED APICAL DOMINANCE1), predicted to span two introns, was isolated from members of Digitalis/Isoplexis. Phylogenetic analyses, under both maximum parsimony and Bayesian inference, were performed and revealed evidence of putative MAX4-like paralogues. The MAX4-like trees were compared with those obtained for Digitalis/Isoplexis using ITS and trnL-F, revealing a high degree of incongruence between these different DNA regions. Network analyses indicate complex patterns of evolution between the MAX4 sequences, which cannot be adequately represented on bifurcating trees. The incidence of paralogy restricts the use of MAX4 in phylogenetic inference within the study group, although MAX4 could potentially be used in combination with other DNA regions for resolving species relationships in cases where paralogues can be clearly identified.

Phylogenetic utility of MORE AXILLARY GROWTH4 (MAX4)-like genes: a case study in Digitalis/Isoplexis (Plantaginaceae)

We present the first assessment of phylogenetic utility of a potential novel low-copy nuclear gene region in flowering plants. A fragment of the MORE AXILLARY GROWTH 4 gene (MAX4, also known as RAMOSUS1 and DECREASED APICAL DOMINANCE1), predicted to span two introns, was isolated from members of Digitalis/Isoplexis. Phylogenetic analyses, under both maximum parsimony and Bayesian inference, were performed and revealed evidence of putative MAX4-like paralogues. The MAX4-like trees were compared with those obtained for Digitalis/Isoplexis using ITS and trnL-F, revealing a high degree of incongruence between these different DNA regions. Network analyses indicate complex patterns of evolution between the MAX4 sequences, which cannot be adequately represented on bifurcating trees. The incidence of paralogy restricts the use of MAX4 in phylogenetic inference within the study group, although MAX4 could potentially be used in combination with other DNA regions for resolving species relationships in cases where paralogues can be clearly identified.

Isolation and characterization of an AINTEGUMENTA-like gene in different coconut (Cocos nucifera L.) varieties from Sri Lanka

Development of an efficient tissue culture protocol in coconut is hampered by numerous technical constraints. Thus a greater understanding of the fundamental aspects of embryogenesis is essential. The role of AINTEGUMENTA-like genes in embryogenesis has been elucidated not only in model plants but also in economically important crops. A coconut gene, CnANT, that encodes two APETALA2 (AP2) domains and a conserved linker region similar to those of the BABY BOOM transcription factor was cloned, characterized, and its tissue specific expression was examined. The full-length cDNA of 1,780 bp contains a 1,425-bp open reading frame that encodes a putative peptide of 474 amino acids. The genomic DNA sequence includes 2,317 bp and consists of nine exons interrupted by eight introns. The exon/intron organization of CnANT is similar to that of homologous genes in other plant species. Analysis of differential tissue expression by real-time polymerase chain reaction indicated that CnANT is expressed more highly in in vitro grown tissues than in other vegetative tissues. Sequence comparison of the genomic sequence of CnANT in different coconut varieties revealed one single nucleotide polymorphism and one indel in the first exon and first intron, respectively, which differentiate the Tall group of trees from Dwarfs. The indel sequence, which can be considered a simple sequence repeats marker, was successfully used to distinguish the Tall and Dwarf groups as well as to develop a marker system, which may be of value in the identification of parental varieties that are used in coconut breeding programs in Sri Lanka.

Development of new nuclear markers and characterization of single nucleotide polymorphisms in kelp gull (Larus dominicanus)

The present study seeks to develop nuclear markers for the kelp gull (Larus dominicanus). We hereby report the characterization of 12 independent nuclear introns, where 104 single nucleotide polymorphisms (SNPs) in 8138 sequenced base pairs were observed. These SNP markers are the first to be designed for genotyping a gull species. The markers will provide useful tools for understanding which processes act or acted upon kelp gulls to cause their low genetic variability in mitochondrial DNA. In addition, these markers open a new opportunity for population genetic and evolutionary studies in the Laridae group.

Oscheius tipulae as an example of eEF1A gene diversity in nematodes

We characterized four eEF1A genes in the alternative rhabditid nematode model organism Oscheius tipulae. This is twice the copy number of eEF1A genes in C. elegans, C. briggsae, and, probably, many other free-living and parasitic nematodes. The introns show features remarkably different from those of other metazoan eEF1A genes. Most of the introns in the eEF1A genes are specific to O. tipulae and are not shared with any of the other genes described in metazoans. Most of the introns are phase 0 (inserted between two codons), and few are inserted in protosplice sites (introns inserted between the nucleotide sequence A/CAG and G/A). Two of these phase 0 introns are conserved in sequence in two or more of the four eEF1A gene copies, and are inserted in the same position in the genes. Neither of these characteristics has been detected in any of the nematode eEF1A genes characterized to date. The coding sequences were also compared with other eEF1A cDNAs from 11 different nematodes to determine the variability of these genes within the phylum Nematoda. Parsimony and distance trees yielded similar topologies, which were similar to those created using other molecular markers. The presence of more than one copy of the eEF1A gene with nearly identical coding regions makes it difficult to define the orthologous cDNAs. As shown by our data on O. tipulae, careful and extensive examination of intron positions in the eEF1A gene across the phylum is necessary to define their potential for use as valid phylogenetic markers.

Molecular characterization of nitrate reductase gene and its expression in the marine red alga Gracilaria tenuistipitata (Rhodophyta)

The enzyme nitrate reductase (NR) responsible for the conversion of nitrate to nitrite is considered to be the rate-limiting step in nitrogen assimilation. The economically important marine macroalga Gracilaria tenuistipitata presents a circadian oscillation in NR protein content and activity. In order to identify if the regulation of NR in G. tenuistipitata happens at transcriptional levels, the NR cDNA and gene were sequenced and the NR mRNA expression was studied. Analysis of the sequenced gene revealed absence of introns which is unusual for NR genes. The transcriptional profiling revealed a circadian rhythm for NR; furthermore, a rhythm was observed in constant light condition, suggesting a possible regulation by the biological clock at the mRNA levels for NR in G. tenuistipitata.

Caracterização molecular dos genes PSO2 e PSO4 de Saccharomyces cerevisiae envolvidos na reparação do DNA : análise funcional e identificação de interações proteína-proteína

O alelo mutante termo-condicionalmente letal pso4-1 do gene PRP19, que codifica uma proteína associada ao spliceossoma, permitiu investigar a influência deste gene no processamento de pré-mRNA, reparação do DNA e esporulação. Fenótipos relacionados a genes portadores de introns foram correlacionados à temperatura. Sistemas repórteres para processamento de pré-mRNA e RT-PCR mostraram que eficiência de processamento de mRNA no mutante pso4-1 é inversamente correlacionada com a temperatura de crescimento. Uma mutação pontual, substituindo uma leucina por uma serina foi identificada dentro da região codificadora N-terminal do alelo Pso4-1 e afeta as propriedades bioquímicas de Pso4-1p. Entre 24 clones isolados utilizando o sistema doishíbridos, 7 foram identificados como partes dos genes RAD2, RLF2 e DBR1. RAD2 codifica uma endonuclease indispensável para a via reparação por excisão de nucleotídeos (NER), RLF2 codifica a subunidade maior do fator de montagem da cromatina I, cuja deleção resulta em sinsibilidade à radiação UVC, enquanto que DBR1 codifica uma enzima que atua sobre substratos de RNA na forma lariat, degradando estruturas lariat em introns durante o processamento de mRNA. A caracterização dos fenótipos após tratamentos com mutágenos em linhagens mutantes simples e duplos de rad2∆, rlf2∆ e pso4-1 mostraram sensibilidade aumentada para para mutantes rad2∆/pso4-1 e rlf2∆/pso4-1, sugerindo uma interferência funcional destas proteínas no processo dereparação do DNA em Saccharomyces cerevisiae. O mecanismo exato de reparação de pontes inter-cadeia (ICL) em S. cerevisiae não é ainda totalmente conhecido. Identificando novos fenótipos e isolando proteínas potencialmente capazes de interagir com Pso2p através da técnica do sistema dois-híbridos, foi possível extender a caracterização deste gene específica para reparação de pontes intercadeia. Tratamentos com acetaldeído (ACA), um metabólito natural da via glicolítica, foi mais tóxico a linhagem mutante pso2 em comparação com a linhagem selvagem e também capaz de induzir a expressão da fusão contendo o promotor de PSO2 à lacZ (PSO2-lacZ) por um fator comparável à tratamentos com outros agentes indutores de ICLs, indicando que o metabólito natural ACA pode causar danos do tipo ICL em S. cerevisiae. A utilização do sistema dois-híbridos permitiu isolar partes de proteínas codificadas por nove diferentes genes, entre eles a proteína quinase Pak1p, um supressor de mutações termosensíveis da DNA Polimerase alfa. Pak1p interage com a extremidade C-terminal conservada de Pso2p, uma região da proteína recentemente nomeada β-CASP entre v ortólogos conhecidos do gene PSO2. A integridade do domínio β-CASP é essencial para a reparaçãode DNA proficiente como demonstrado em ensaios de complementação com mutantes pso2 ∆. Comparação da sobrevivência após tratamento com agentes mutagênicos de simples mutantes pso2 ∆ e pak1 ∆ assim com o dulpo mutante pso2 ∆/pak1 ∆ revelaram que o gene PAK1 é necessário para reparação do DNA proficiente como na linhagem selvagem. A interação epistática dos dois alelos mutantes na linhagem duplo mutante sugere que Pak1p atua na mesma via de reparação a qual PSO2 pertence e que PAK1 constitui um novo locus envolvido na reparação do DNA em S. cerevisiae.