Fungal Smn and Spf30 homologues are mainly present in filamentous fungi and genomes with many introns: implications for spinal muscular atrophy

Spinal muscular atrophy is an important rare genetic disease characterized by the loss of motor neurons, where the main gene responsible is smn1. Orthologous genes have only been characterized in a single fungal genome: Schizosaccharomyces pombe. We have searched for putative SMN orthologues in publically available fungal genomes, finding that they are predominately present in filamentous fungi. SMN binding partners and the SPF30 SMN paralogue, which are all involved in mRNA splicing, were found to be present in a similar but non-identical subset of fungal genomes. The Saccharomycces cerevisiae yeast genome contains neither smn1 orthologues nor paralogues and it has been suggested that this might be related to the low number of introns in this yeast. Here we have tested this hypothesis by looking at other fungal genomes. Significantly, we find that fungal genomes with high numbers of introns also possess an SMN orthologue or at least its paralogue, SPF30.     

The bphDEF meta-cleavage pathway genes involved in biphenyl/polychlorinated biphenyl degradation are located on a linear plasmid and separated from the initial bphACB genes in Rhodococcus sp. strain RHA1

The bphACB genes responsible for the initial oxidation of the aromatic ring of biphenyl/polychlorinated biphenyls (PCB) to meta-cleavage product in Rhodococcus sp. RHA1 have been characterized. We cloned the 6.1 kb EcoRI fragment containing another extradiol dioxygenase gene (etbC) which was induced during the growth on ethylbenzene. The bphD, bphE and bphF encoding 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPD) hydrolase, 2-hydroxypenta-2,4-dienoate hydratase and 4-hydroxy-2-oxovalerate aldolase, respectively, were found downstream of etbC. The deduced amino acid (aa) sequence of RHA1 bphD and bphE had 27–33% and 32–38% identity, respectively, with those of the corresponding genes in Pseudomonas. BphE and BphF are closely related to the corresponding homoprotocatechuate meta-cleavage pathway enzymes of Escherichia coli C. The bphD and bphF were expressed in E. coli and the BphD activity was detected. The etbCbphDEF genes were transcribed in biphenyl and ethylbenzene growing cells. Pulsed field gel electrophoresis (PFGE) analysis indicated that RHA1 contains three large linear plasmids. Southern blot analysis indicated that the meta-cleavage pathway for biphenyl/PCB catabolism in RHA1 is directed by the 390 kb plasmid borne bphDEF genes located separately from bphACB gene cluster on the 1100 kb plasmid.     

Identification of Dmrt genes and their up-regulation during gonad transformation in the swamp eel (Monopterus albus)

The swamp eel is a teleost fish with a characteristic of natural sex reversal and an ideal model for vertebrate sexual development. However, underlying molecular mechanisms are poorly understood. We report the identification of five DM (doublesex and mab-3) domain genes in the swamp eel that include Dmrt2, Dmrt2b, Dmrt3, Dmrt4 and Dmrt5, which encode putative proteins of 527, 373, 471, 420 and 448 amino acids, respectively. Phylogenetic tree showed that these genes are clustered into corresponding branches of the DM genes in vertebrates. Southern blot analysis indicated that the Dmrt1–Dmrt3–Dmrt2 genes are tightly linked in a conserved gene cluster. Notably, these Dmrt genes are up-regulated during gonad transformation. Furthermore, mRNA in situ hybridisation showed that Dmrt2, Dmrt3, Dmrt4 and Dmrt5 are expressed in developing germ cells. These results are evidence that the DM genes are involved in sexual differentiation in the swamp eel.     

Phylogenetic estimation of Sciaenidae in the East China Sea inferred from nuclear EPIC DNA sequence variation

Here we describe a phylogenetic analysis of sciaenids of the East China Sea based on nuclear exon-primed intron-crossing genes (EPIC markers) and a mitochondrial gene (CO1). Separate analyses of the two data partitions resulted in mostly congruent trees. Although there were some differences in the classification of these species, the main difference between trees obtained by the mitochondrial gene (CO1) and nuclear DNA sequences was the position of Miichthys miiuy and Johnius belangerii. In the mitochondrial phylogeny, Johnius belangerii was placed at the most basal position forming an individual clade, while other species formed another large cluster. Miichthys miiuy formed an independent basal sub-clade grouped with Larimichthys and Collichthys. Collichthys lucidus was grouped with Larimichthys crocea and Larimichthys polyactis. Trees based on the nuclear genes differed somewhat from those based on the CO1 mitochondrial gene. In this analysis, two groups resulted, the Larimichthys and Collichthys clade, and another clade including a total of five species: Johnius belangerii, Nibea albiflora, Pennahia argentata, Sciaenops ocellatus, and Argyrosomus japonicus; Johnius belangerii clustered with Nibea albiflora. Miichthys miiuy was placed at the basal position of the other cluster because it was an independent basal sub-clade grouped with Johnius belangerii, Nibea albiflora, Pennahia argentata, Sciaenops ocellatus, and Argyrosomus japonicus. Many aspects of the phylogeny of the Sciaenidae remain unresolved, and further analysis based on more molecular information and extensive taxon sampling is necessary to elucidate the phylogenetic relationships among the major lineages within Sciaenidae.     

A cluster of at least three esterase genes inLucilia cuprina includes malathion carboxylesterase and two other esterases implicated in resistance to organophosphates

Three distinct malathion carboxylesterase (MCE) phenotypes have been identified among strains ofLucilia cuprina. The high-activity phenotype shows 1.6-and 33-fold more MCE specific activity than the intermediate- and low-activity phenotypes, respectively. Flies with high MCE activity are 1000-fold more resistant to malathion than flies with either low or intermediate MCE phenotypes, which are equally susceptible. High and low MCE specific activity are allelic and encoded by theRmal gene on chromosome 4.Rmal is clustered within one map unit of two other esterase genes,Rop1 andE9, which are implicated in resistance to other organophosphate insecticides. Intermediate MCE specific activity is also inherited within the cluster, although its allelism toRmal, Rop1, orE9 is unclear. The cluster does not contain the gene for the hemolymph esterase E4, which maps 6.1 map units fromRop1, on the other side of thebubbled wing marker. The cluster appears to be homologous to part of a tandem array of 11 esterase genes on chromosome 3R ofDrosophila melanogaster.     

Cloning and Characterization of Two Pyruvate Decarboxylase Genes from Pichia stipitis CBS 6054

In Pichia stipitis, fermentative and pyruvate decarboxylase (PDC) activities increase with diminished oxygen rather than in response to fermentable sugars. To better characterize PDC expression and regulation, two genes for PDC (PsPDC1 and PsPDC2) were cloned and sequenced from P. stipitis CBS 6054. Aside from Saccharomyces cerevisiae, from which three PDC genes have been characterized, P. stipitis is the only organism from which multiple genes for PDC have been identified and characterized. PsPDC1 and PsPDC2 have diverged almost as far from one another as they have from the next most closely related known yeast gene. PsPDC1 contains an open reading frame of 1,791 nucleotides encoding 597 amino acids. PsPDC2 contains a reading frame of 1,710 nucleotides encoding 570 amino acids. An 81-nucleotide segment in the middle of the β domain of PsPDC1 codes for a unique segment of 27 amino acids, which may play a role in allosteric regulation. The 5′ regions of both P. stipitis genes include two putative TATA elements that make them similar to the PDC genes from S. cerevisiae, Kluyveromyces marxianus, and Hanseniaspora uvarum.     

Expression of floral MADS-box genes in Sinofranchetia chinensis (Lardizabalaceae): implications for the nature of the nectar leaves

Background and Aims

The perianths of the Lardizabalaceae are diverse. The second-whorl floral organs of Sinofranchetia chinensis (Lardizabalaceae) are nectar leaves. The aim of this study was to explore the nature of this type of floral organ, and to determine its relationship to nectar leaves in other Ranunculales species, and to other floral organs in Sinofranchetia chinensis.

Methods

Approaches of evolutionary developmental biology were used, including 3′ RACE (rapid amplification of cDNA ends) for isolating floral MADS-box genes, phylogenetic analysis for reconstructing gene evolutionary history, in situ hybridization and tissue-specific RT-PCR for identifying gene expression patterns and SEM (scanning electron microscopy) for observing the epidermal cell morphology of floral organs.

Key Results

Fourteen new floral MADS-box genes were isolated from Sinofranchetia chinensis and from two other species of Lardizabalaceae, Holboellia grandiflora and Decaisnea insignis. The phylogenetic analysis of AP3-like genes in Ranunculales showed that three AP3 paralogues from Sinofranchetia chinensis belong to the AP3-I, -II and -III lineages. In situ hybridization results showed that SIchAP3-3 is significantly expressed only in nectar leaves at the late stages of floral development, and SIchAG, a C-class MADS-box gene, is expressed not only in stamens and carpels, but also in nectar leaves. SEM observation revealed that the adaxial surface of nectar leaves is covered with conical epidermal cells, a hallmark of petaloidy.

Conclusions

The gene expression data imply that the nectar leaves in S. chinensis might share a similar genetic regulatory code with other nectar leaves in Ranunculales species. Based on gene expression and morphological evidence, it is considered that the nectar leaves in S. chinensis could be referred to as petals. Furthermore, the study supports the hypothesis that the nectar leaves in some Ranunculales species might be derived from stamens.     

The complete genome of Burkholderia phenoliruptrix strain BR3459a,a symbiont of Mimosa flocculosa: highlighting the coexistence of symbiotic and pathogenic genes

Background

Burkholderia species play an important ecological role related to xenobiosis, the promotion of plant growth, the biocontrol of agricultural diseases, and symbiotic and non-symbiotic biological nitrogen fixation. Here, we highlight our study as providing the first complete genome of a symbiotic strain of B. phenoliruptrix, BR3459a (=CLA1), which was originally isolated in Brazil from nodules of Mimosa flocculosa and is effective in fixing nitrogen in association with this leguminous species.

Results

Genomic comparisons with other pathogenic and non-pathogenic Burkholderia strains grouped B. phenoliruptrix BR3459a with plant-associated beneficial and environmental species, although it shares a high percentage of its gene repertoire with species of the B. cepacia complex (Bcc) and "pseudomallei" group. The genomic analyses showed that the bce genes involved in exopolysaccharide production are clustered together in the same genomic region, constituting part of the Group III cluster of non-pathogenic bacteria. Regarding environmental stresses, we highlight genes that might be relevant in responses to osmotic, heat, cold and general stresses. Furthermore, a number of particularly interesting genes involved in the machinery of the T1SS, T2SS, T3SS, T4ASS and T6SS secretion systems were identified. The xenobiotic properties of strain BR3459a were also investigated, and some enzymes involved in the degradation of styrene, nitrotoluene, dioxin, chlorocyclohexane, chlorobenzene and caprolactam were identified. The genomic analyses also revealed a large number of antibiotic-related genes, the most important of which were correlated with streptomycin and novobiocin. The symbiotic plasmid showed high sequence identity with the symbiotic plasmid of B. phymatum. Additionally, comparative analysis of 545 housekeeping genes among pathogenic and non-pathogenic Burkholderia species strongly supports the definition of a new genus for the second branch, which would include BR3459a.

Conclusions

The analyses of B. phenoliruptrix BR3459a showed key property of fixing nitrogen that together with genes for high tolerance to environmental stresses might explain a successful strategy of symbiosis in the tropics. The strain also harbours interesting sets of genes with biotechnological potential. However, the resemblance of certain genes to those of pathogenic Burkholderia raise concerns about large-scale applications in agriculture or for bioremediation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-535) contains supplementary material, which is available to authorized users.     

Complete mitochondrial genome sequences of the three pelagic chaetognaths Sagitta nagae,Sagitta decipiens and Sagitta enflata

The complete nucleotide sequences of the mitochondrial genomes were determined for the three pelagic chaetognaths, Sagitta nagae, Sagitta decipiens, and Sagitta enflata. The mitochondrial genomes of these species which were 11,459, 11,121, and 12,631 bp in length, respectively, contained 14 genes (11 protein-coding genes, one transfer RNA gene, and two ribosomal RNA genes), and were found to have lost 23 genes that are present in the typical metazoan mitochondrial genome. The same mitochondrial genome contents have been reported from the benthic chaetognaths belonging to the family Spadellidae, Paraspadella gotoi and Spadella cephaloptera. Within the phylum Chaetognatha, Sagitta and Spadellidae are distantly related, suggesting that the gene loss occurred in the ancestral species of the phylum. The gene orders of the three Sagitta species are markedly different from those of the other non-Chaetognatha metazoans. In contrast to the region with frequent gene rearrangements, no gene rearrangements were observed in the gene cluster encoding COII–III, ND1–3, srRNA, and tRNA^met. Within this conserved gene cluster, gene rearrangements were not observed in the three Sagitta species or between the Sagitta and Spadellidae species. The gene order of this cluster was also assumed to be the ancestral state of the phylum.     

Characterization of glucuronic acid containing glycolipid in Aspergillus fumigatus mycelium

A glucuronic acid containing glycerolipid was isolated from the filamentous fungi Aspergillus fumigatus. This acidic glycolipid was extracted from the membrane of mycelium and purified by two successive chromatographic steps on DEAE-Sephadex and Silica columns. Chemical structural analysis was performed using methylation, gas-chromatography, gas-chromatography-mass spectrometry, nano-electrospray mass spectrometry and ¹H/¹³C NMR spectra. The corresponding structure is a 3-(O-α-glucuronyl)-1,2-diacyl-sn-glycerol, where acyl chains are mainly C_16:0, C_18:0, C_18:1, and C_18:2. This α-GlcA-diacylglycerol is not present in fungal conidia. This acidic glycerolipid is described here for the first time in a fungal species. Two homologs of UDP-glucose dehydrogenase that convert UDP-glucose into UDP-glucuronic acid, are present in A. fumigatus genome, UGD1 and UGD2. Gene deletion showed that only UGD1 is essential for the biosynthesis of GlcA-DG. However, no particular phenotype has been observed in the Ugd1Δ mutant. Biological function of this acidic glycolipid remains unknown in A. fumigatus.