Evolution of the secondary symbiont "Candidatus serratia symbiotica" in aphid species of the subfamily lachninae

Buchnera aphidicola BCc, the primary endosymbiont of the aphid Cinara cedri (subfamily Lachninae), is losing its symbiotic capacity and might be replaced by the coresident "Candidatus Serratia symbiotica." Phylogenetic and morphological analyses within the subfamily Lachninae indicate two different "Ca. Serratia symbiotica" lineages and support the longtime coevolution of both symbionts in C. cedri.     

In vivo evidence for a regulatory role of the kinase activity of the <Emphasis Type="Italic">linotte</Emphasis>/<Emphasis Type="Italic">derailed</Emphasis> receptor tyrosine kinase,a <Emphasis Type="Italic">Drosophila</Emphasis> Ryk ortholog

The RYK subfamily of receptor tyrosine kinases is characterised by unusual, but highly conserved, amino acid substitutions in the kinase domain. The linotte/derailed gene encodes a Drosophila RYK subfamily member involved in embryonic and adult central nervous system development. Previous studies have shown that the kinase activity of this receptor is not required in vivo for its embryonic function. In this study, we have investigated the role of the cytoplasmic domain and the kinase activity of the linotte/derailed receptor tyrosine kinase in adult brain development. Our results indicate that these domains are not essential for adult brain development but they are required for the proper regulation of the activity of this receptor. This sheds light on a regulatory role for the kinase activity of a RYK subfamily member.Edited by C DesplanEmmanuel Taillebourg and Caroline Moreau-Fauvarque contributed equally to this work     

The COBRA gene family in <Emphasis Type="Italic">Populus</Emphasis> and gene expression in vegetative organs and in response to hormones and environmental stresses

COBRA proteins have been shown to be involved in both cell wall expansion and/or cellulose deposition. In this paper, we analyzed all 18 COBRA genes (PtCOBRA) from the completely sequenced Populus trichocarpa genome. The 14-member PtCOBRA subfamily I proteins have high similarities to the Arabidopsis (At) COB subfamily, and members with full length sequences were predicted to possess significant potentials for a GPI-anchor site. The 4-member PtCOBRA subfamily II proteins are 45% longer than subfamily I proteins and lack ω-attachment sites at the C terminus, and are more similar to AtCOBL7 subfamily. The expression of the Populus COBRA family genes were regulated in a tissue-specific manner, and were shown to also respond differentially to inductions of hormones and environmental stimuli which affect plant cell expansion. The high levels of expressions, particularly in shoot tip and young root organs, suggests that at least some Populus COBRA genes are likely involved in regulating cell expansion.     

An unexpectedly high degree of specialization and a widespread involvement in sterol metabolism among the <Emphasis Type="Italic">C. elegans</Emphasis> putative aminophospholipid translocases

Background  

P-type ATPases in subfamily IV are exclusively eukaryotic transmembrane proteins that have been proposed to directly translocate the aminophospholipids phosphatidylserine and phosphatidylethanolamine from the exofacial to the cytofacial monolayer of the plasma membrane. Eukaryotic genomes contain many genes encoding members of this subfamily. At present it is unclear why there are so many genes of this kind per organism or what individual roles these genes perform in organism development.     

Isolation and characterization of seventy-nine full-length <Emphasis Type="Italic">mariner</Emphasis>-like transposase genes in the Bambusoideae subfamily

Mariner-like elements (MLEs) are the most diverse and widespread transposable elements, with members of the MLE superfamily found in fungi, plants, ciliates and animals. In a previous study, we characterized 82 MLE transposase gene fragments (average length 383 bp) in 44 bamboo species, indicating that MLEs are widespread, abundant and diverse in the Bambusoideae subfamily. In this study, we isolated 79 full-length MLE transposase genes from 63 bamboo species representing 38 genera in six subtribes mainly found in China. The transposases were highly conserved, mostly uniform in length and contained intact DNA-binding motifs and DD39D catalytic domains with few notable frameshift, indel and nonsense mutations. This suggested the MLEs are probably still mobile, not yet affected by vertical inactivation. A phylogenetic tree of the Bambusoideae subfamily established using ribosomal DNA internal transcribed spacer sequences was incongruent with a second tree based on the MLE transposase genes. This evidence, together with the presence of near-identical MLEs in distantly related species and diverse MLEs in closely related species, indicates that MLEs have evolved in a distinct manner, probably independently of speciation events in the subfamily. The evolution and diversity of MLE transposase genes in the Bambusoideae subfamily is discussed.     

Relationships among "ancient araliads" and their significance for the systematics of Apiales

The relationship between the angiosperm families Apiaceae and Araliaceae (order Apiales) has been difficult to resolve, due in large part to problems associated with taxa characterized by a mixture of features typical of both families. Among such confounding groups are the araliads Delarbrea, Pseudosciadium, Myodocarpus, Mackinlaya, and Apiopetalum and many members of Apiaceae subfamily Hydrocotyloideae. Traditional systems have often envisioned these taxa as phyletic intermediates or bridges between the two families. To reevaluate the phylogenetic position of the "intermediate" araliad genera, molecular data were collected from nuclear (rDNA ITS) and plastid (matK) sequences from a complete or near-complete sampling of species in each genus. When analyzed with samples representing the other major clades now recognized within Apiales, results confirm and expand the findings of previously published studies. The five araliad "intermediates" are placed within two well-supported clades clearly segregated from the "core" groups of both Apiaceae and Araliaceae. These segregate clades closely parallel traditional definitions of the araliad tribes Myodocarpeae (Delarbrea, Pseudosciadium, and Myodocarpus) and Mackinlayeae (Mackinlaya and Apiopetalum), and relationships among the species within these clades are largely supported by morphological and anatomical data. Based on these results, Myodocarpeae and Mackinlayeae may best be treated as distinct families. This approach would render four monophyletic groups within Apiales, to which a fifth, Pittosporaceae, cannot at present be excluded. Sampling of taxa from Hydrocotyloideae remains preliminary, but results confirm previous studies indicating the polyphyly of this subfamily: hydrocotyloid taxa may be found in no fewer than three major clades in Apiales.     

<Emphasis Type="Italic">Germin-like protein</Emphasis> gene family of a moss, <Emphasis Type="Italic">Physcomitrella patens</Emphasis>, phylogenetically falls into two characteristic new clades

We identified 77 EST clones encoding germin-like proteins (GLPs) from a moss, Physcomitrella patens in a database search. These Physcomitrella GLPs (PpGLPs) were separated into seven groups based on DNA sequence homology. Phylogenetic analysis showed that these groups were divided into two novel clades clearly distinguishable from higher plant germins and GLPs, named bryophyte subfamilies 1 and 2. PpGLPs belonging to bryophyte subfamilies 1 lacked two cysteines at the conserved positions observed in higher plant germins or GLPs. PpGLPs belonging to bryophyte subfamily 2 contained two cysteines as observed in higher plant germins and GLPs. In bryophyte subfamily 1, 12 amino acids, in which one of two cysteines is included, were deleted between boxes A and B. Further, we determined the genomic structure of all of seven PpGLP genes. The sequences of PpGLPs of bryophyte subfamily 1 contained one or two introns, whereas those of bryophyte subfamily 2 contained no introns. Other GLPs from bryophytes, a liverwort GLP from Marchantia polymorpha, and two moss GLPs from Barbula unguiculata and Ceratodon purpureus also fell into bryophyte subfamily 1 and bryophyte subfamily 2, respectively. No higher plant germins and GLPs were grouped into the bryophyte subfamilies 1 and 2 by our analysis. Moreover, we revealed that PpGLP6 had manganese-containing extracellular superoxide dismutase activity. These results indicated that bryophyte possess characteristic GLPs, which phylogenetically are clearly distinguishable from higher plant GLPs.     

鲤科鲌亚科鱼类的系统发育及动物地理学

以雅罗鱼亚科为外群,采用分支系统学的原理和方法对鲌亚科17个属(须鳊属除外)进行了系统发育和动物地理学的分析.结果表明,(1)鲌亚科这17个属为一个单系群,并由4个较小的单系群组成;(2)鲌亚科现在的地理分布格局除源自离散事件外,主要源于扩散事件.鲌亚科的特征演化还表明,东亚地区地质历史的反转演化和平行演化可能在鲌亚科系统发育过程中起了重要的作用.     

The evolutionary history of <Emphasis Type="Italic">mariner</Emphasis>-like elements in Neotropical drosophilids

The evolutionary history of mariner-like elements (MLEs) in 49 mainly Neotropical drosophilid species is described. So far, the investigations about the distribution of MLEs were performed mainly using hybridization assays with the Mos1 element (the first mariner active element described) in a widely range of drosophilid species and these sequences were found principally in species that arose in Afrotropical and Sino-Indian regions. Our analysis in mainly Neotropical drosophilid species shows that twenty-three species presented MLEs from three different subfamilies in their genomes: eighteen species had MLEs from subfamily mellifera, fifteen from subfamily mauritiana and three from subfamily irritans. Eleven of these species exhibited elements from more than one subfamily in their genome. In two subfamilies, the analyzed coding region was uninterrupted and contained conserved catalytic motifs. This suggests that these sequences were probably derived from active elements. The species with these putative active elements are Drosophila mediopunctata and D. busckii for the mauritiana subfamily, and D. paramediostriata for the mellifera subfamily. The phylogenetic analysis of MLE, shows a complex evolutionary pattern, exhibiting vertical transfer, stochastic loss and putative events of horizontal transmission occurring between different Drosophilidae species, and even those belonging to more distantly related taxa such as Bactrocera tryoni (Tephritidae family), Sphyracephala europaea (Diopsoidea superfamily) and Buenoa sp. (Hemiptera order). Moreover, our data show that the distribution of MLEs is not restricted to Afrotropical and Sino-Indian species. Conversely, these TEs are also widely distributed in drosophilid species arisen in the Neotropical region.     

In silico characterization of the INO80 subfamily of SWI2/SNF2 chromatin remodeling proteins

Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The yeast Ino80, the catalytic ATPase subunit of the INO80 complex, is the most recently described member of the SNF2 family. Outside the conserved ATPase domain, it has very little similarity with other well-characterized SNF2 proteins hence it is believed to represent a new subfamily. We have identified new members of this subfamily in different organisms and have detected characteristic features of this subfamily. Using various data mining tools we have identified a new, previously undetected domain in all members of this subfamily. This domain designated DBINO is characteristic of the INO80 subfamily and is predicted to have DNA-binding function. The presence of this domain in all the INO80 subfamily proteins from different organisms suggests its conserved function in evolution.     

Bacteriophages LIMElight and LIMEzero of Pantoea agglomerans, belonging to the "phiKMV-like viruses"

Pantoea agglomerans is a common soil bacterium used in the biocontrol of fungi and bacteria but is also an opportunistic human pathogen. It has been described extensively in this context, but knowledge of bacteriophages infecting this species is limited. Bacteriophages LIMEzero and LIMElight of P. agglomerans are lytic phages, isolated from soil samples, belonging to the Podoviridae and are the first Pantoea phages of this family to be described. The double-stranded DNA (dsDNA) genomes (43,032 bp and 44,546 bp, respectively) encode 57 and 55 open reading frames (ORFs). Based on the presence of an RNA polymerase in their genomes and their overall genome architecture, these phages should be classified in the subfamily of the Autographivirinae, within the genus of the "phiKMV-like viruses." Phylogenetic analysis of all the sequenced members of the Autographivirinae supports the classification of phages LIMElight and LIMEzero as members of the "phiKMV-like viruses" and corroborates the subdivision into the different genera. These data expand the knowledge of Pantoea phages and illustrate the wide host diversity of phages within the "phiKMV-like viruses."     

Courtship and Mating Behavior of the Cockroach <Emphasis Type="Italic">Oxyhaloa deusta</Emphasis> [Thunberg, 1784] (Blaberidae,Oxyhaloinae): Attraction Bioassays and Morphology of the Pheromone Sources

In this paper, we focus on the reproductive behavior of the cockroach Oxyhaloa deusta. Within the Oxyhaloinae subfamily, mating strategies and glandular areas involved in pheromone production have been studied for several genera belonging to the Nauphoetini and Gromphadorhini tribes. However, this is the first time that courtship and mating behavior have been explored within the genus Oxyhaloa, and in a more general way within the Oxyhaloini tribe. This work, comprising behavioral observations, olfactometric bio-assays and morphological data, highlights unusual behaviors and novelties in potential sex pheromone gland location, in both males (tergite 8) and females (supra-valvular area). Surprisingly, our results also indicate that mate finding is initiated by the female. This is quite remarkable inasmuch as the Oxyhaloinae subfamily is the only cockroach group in which males initiate mate finding by means of a sex pheromone, emitted during the calling posture by extending abdominal tergites. In the Oxyhaloinae subfamily, this occurrence of various reproductive behavioral patterns (including all the mating patterns known at present in Blattaria) in closely-related species is striking, and makes this group a suitable model for studying the changes in mating behavior correlated with the location of sexual glands.     

A cold-adapted extracellular serine proteinase of the yeast<Emphasis Type="Italic"> Leucosporidium antarcticum</Emphasis>

An extracellular serine proteinase, lap2, from the psychrophilic antarctic yeast Leucosporidium antarcticum 171 was purified to homogeneity and characterized. The enzyme is a glycoprotein with a molecular mass of 34.4 kDa and an isoelectric point of pH 5.62. The proteinase is halotolerant, and its activity and stability are dependent neither on Ca²⁺ nor on other metal ions. Lap2 is a true psychrophilic enzyme because of low optimal temperature (25°C), poor thermal stability, relatively small values of free energy, enthalpy and entropy of activation, and high catalytic efficiency at 0–25°C. The 35 N-terminal amino acid residues of lap2 have homology with subtilases of the proteinase K subfamily (clan SB, family S8, subfamily C). The proteinase lap2 is the first psychrophilic subtilase in this family.Communicated by K. Horikoshi     

Close linkage of the cytochrome P450IIA gene subfamily (Cyp2a) to Cyp2b and Coh on mouse chromosome 7

The cytochrome P450IIB gene subfamily (Cyp2b) has previously been mapped close to the Coh locus encoding a cytochrome P450 with coumarin 7-hydroxylase (COH) activity on mouse chromosome 7. Given this observation, it had been considered that COH was a member of the P450IIB subfamily. However, recent biochemical and cDNA expression experiments indicate that a member of the P450IIA subfamily, rather than of the P450IIB subfamily, encodes COH. We have resolved this apparent anomaly between the genetic and biochemical data by showing that genes from the P450IIA subfamily (Cyp2a) are closely linked to Coh and to Cyp2b on mouse chromosome 7.     

The Pif1p subfamily of helicases: region-specific DNA helicases?

DNA helicases are required for DNA replication, recombination and repair. Despite a common enzymatic function - the ability to unwind duplex DNA - most helicases share only limited amino acid sequence similarity. Helicases that have significant sequence similarity define a subfamily. It remains unclear, however, how this sequence similarity relates to helicase function. The Saccharomyces cerevisiae Pif1p helicase is the prototype member of a helicase subfamily that is conserved from yeasts to humans. As the two Pif1p subfamily members studied to date affect the same DNA sequences, the amino acid similarity that defines this subfamily might reflect common substrates.     

Parhadrestiinae, a new subfamily for Parhadrestia James and Cretaceogaster Teskey (Diptera: Stratiomyidae)

Abstract. A new subfamily of Stratiomyidae is proposed for Parhadrestia James and Cretaceogaster Teskey (fossil from Upper Cretaceous Canadian amber). Evidence is delimited that indicates that this subfamily is the sister-group to all other known stratiomyids. Taxa in the subfamily are systematically described, including a new species, Parhadrestia curico , from Chile.     

Ecological niches of pathogenic micromycetes of berry plants of subfamily Vaccinioideae

The main and auxiliary first- and second-order ecological niches of the pathogenic micromycetes parasitizing on the berry plants of subfamily Vaccinioideae subfamily is analyzed in this paper.