The tightly regulated promoter of the xanA gene of Aspergillus nidulans is included in a helitron

Helitrons: genomic parasites that generate developmental novelties

Helitrons, classified as DNA transposons, employ rolling-circle intermediates for transposition. Distinguishing themselves from other DNA transposons, they leave the original template element unaltered during transposition, which has led to their characterization as 'peel-and-paste elements'. Helitrons possess the ability to capture and mobilize host genome fragments, with enormous consequences for host genomes. This review discusses the current understanding of Helitrons, exploring their origins, transposition mechanism, and the extensive repercussions of their activity on genome structure and function. We also explore the evolutionary conflicts stemming from Helitron-transposed gene fragments and elucidate their domestication for regulating responses to environmental challenges. Looking ahead, further research in this evolving field promises to bring interesting discoveries on the role of Helitrons in shaping genomic landscapes.

Evolutionarily distinct and sperm-specific supersized chromatin loops are marked by Helitron transposons in Xenopus tropicalis

Transposable elements (TEs) are abundant in metazoan genomes and have multifaceted effects on host fitness. However, the mechanisms underlying the functions of TEs are still not fully understood. Here, we combine Hi-C, ATAC-seq, and ChIP-seq assays to report the existence of multimegabase supersized loop (SSL) clusters in the Xenopus tropicalis sperm. We show that SSL anchors are inaccessible and devoid of the architectural protein CTCF, RNA polymerase II, and modified histones. Nearly all SSL anchors are marked by Helitrons, a class II DNA transposon. Molecular dynamics simulations indicate that SSL clusters are likely formed via a molecular agent-mediated chromatin condensation process. However, only slightly more SSL anchor-associated genes are expressed at late embryo development stages, suggesting that SSL anchors might only function in sperm. Our work shows an evolutionarily distinct and sperm-specific genome structure marked by a subset of Helitrons, whose establishment and function remain to be explored.

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.

A reciprocal translocation involving Aspergillus nidulans snxAHrb1/Gbp2 and gyfA uncovers a new regulator of the G2-M transition and reveals a role in transcriptional repression for the setBSet2 histone H3-lysine-36 methyltransferase

Aspergillus nidulans snxA, an ortholog of Saccharomyces cerevisiae Hrb1/Gbp2 messenger RNA shuttle proteins, is-in contrast to budding yeast-involved in cell cycle regulation, in which snxA1 and snxA2 mutations as well as a snxA deletion specifically suppress the heat sensitivity of mutations in regulators of the CDK1 mitotic induction pathway. snxA mutations are strongly cold sensitive, and at permissive temperature snxA mRNA and protein expression are strongly repressed. Initial attempts to identify the causative snxA mutations revealed no defects in the SNXA protein. Here, we show that snxA1/A2 mutations resulted from an identical chromosome I-II reciprocal translocation with breakpoints in the snxA first intron and the fourth exon of a GYF-domain gene, gyfA. Surprisingly, a gyfA deletion and a reconstructed gyfA translocation allele suppressed the heat sensitivity of CDK1 pathway mutants in a snxA+ background, demonstrating that 2 unrelated genes, snxA and gyfA, act through the CDK1-CyclinB axis to restrain the G2-M transition, and for the first time identifying a role in G2-M regulation for a GYF-domain protein. To better understand snxA1/A2-reduced expression, we generated suppressors of snxA cold sensitivity in 2 genes: (1) loss of the abundant nucleolar protein Nsr1/nucleolin bypassed the requirement for snxA and (2) loss of the Set2 histone H3 lysine36 (H3K36) methyltransferase or a nonmethylatable histone H3K36L mutant rescued hypomorphic snxA mutants by restoring full transcriptional proficiency, indicating that methylation of H3K36 acts normally to repress snxA transcription. These observations are in line with known Set2 functions in preventing excessive and cryptic transcription of active genes.

A complete nicotinate degradation pathway in the microbial eukaryote Aspergillus nidulans

Several strikingly different aerobic and anaerobic pathways of nicotinate breakdown are extant in bacteria. Here, through reverse genetics and analytical techniques we elucidated in Aspergillus nidulans, a complete eukaryotic nicotinate utilization pathway. The pathway extant in this fungus and other ascomycetes, is quite different from bacterial ones. All intermediate metabolites were identified. The cognate proteins, encoded by eleven genes (hxn) mapping in three clusters are co-regulated by a specific transcription factor. Several enzymatic steps have no prokaryotic equivalent and two metabolites, 3-hydroxypiperidine-2,6-dione and 5,6-dihydroxypiperidine-2-one, have not been identified previously in any organism, the latter being a novel chemical compound. Hydrolytic ring opening results in α-hydroxyglutaramate, a compound not detected in analogous prokaryotic pathways. Our earlier phylogenetic analysis of Hxn proteins together with this complete biochemical pathway illustrates convergent evolution of catabolic pathways between fungi and bacteria.

Calling large indels in 1047 Arabidopsis with IndelEnsembler

Large indels greatly impact the observable phenotypes in different organisms including plants and human. Hence, extracting large indels with high precision and sensitivity is important. Here, we developed IndelEnsembler to detect large indels in 1047 Arabidopsis whole-genome sequencing data. IndelEnsembler identified 34 093 deletions, 12 913 tandem duplications and 9773 insertions. Our large indel dataset was more comprehensive and accurate compared with the previous dataset of AthCNV (1). We captured nearly twice of the ground truth deletions and on average 27% more ground truth duplications compared with AthCNV, though our dataset has less number of large indels compared with AthCNV. Our large indels were positively correlated with transposon elements across the Arabidopsis genome. The non-homologous recombination events were the major formation mechanism of deletions in Arabidopsis genome. The Neighbor joining (NJ) tree constructed based on IndelEnsembler's deletions clearly divided the geographic subgroups of 1047 Arabidopsis. More importantly, our large indels represent a previously unassessed source of genetic variation. Approximately 49% of the deletions have low linkage disequilibrium (LD) with surrounding single nucleotide polymorphisms. Some of them could affect trait performance. For instance, using deletion-based genome-wide association study (DEL-GWAS), the accessions containing a 182-bp deletion in AT1G11520 had delayed flowering time and all accessions in north Sweden had the 182-bp deletion. We also found the accessions with 65-bp deletion in the first exon of AT4G00650 (FRI) flowered earlier than those without it. These two deletions cannot be detected in AthCNV and, interestingly, they do not co-occur in any Arabidopsis thaliana accession. By SNP-GWAS, surrounding SNPs of these two deletions do not correlate with flowering time. This example demonstrated that existing large indel datasets miss phenotypic variations and our large indel dataset filled in the gap.

Characterization of a novel Helitron family in insect genomes: insights into classification, evolution and horizontal transfer

Background

Helitrons play an important role in shaping eukaryotic genomes due to their ability to transfer horizontally between distantly related species and capture gene fragments during the transposition. However, the mechanisms of horizontal transfer (HT) and the process of gene fragment capturing of Helitrons still remain to be further clarified.

Results

Here, we characterized a novel Helitron family discontinuously distributed in 27 out of 256 insect genomes. The most prominent characteristic of Hel1 family is its high sequence similarity among species of different insect orders. Related elements were also identified in two spiders, representing the first report of spider Helitrons. All these elements were classified into 2 families, 9 subfamilies and 35 exemplars based on our new classification criteria. Autonomous partners of Helitron were reconstructed in the genomes of three insects and one spider. Integration pattern analysis showed that majority of Hel1A elements in Papilio xuthus and Pieris rapae inserted into introns. Consistent with filler DNA model, stepwise sequence acquisition was observed in Sfru_Hel1Aa, Sfru_Hel1Ab and Sfru_Hel1Ac in Spodoptera frugiperda. Remarkably, the evidence that Prap_Hel1Aa in a Lepdidoptera insect, Pieris rapae, was derived from Cves_Hel1Aa in a parasitoid wasp, Cotesia vestalis, suggested the role of nonregular host-parasite interactions in HT of Helitrons.

Conclusions

We proposed a modified classification criteria of Helitrons based on the important role of the 5′-end of Helitrons in transposition, and provided evidence for stepwise sequence acquisition and recurrent HT of a novel Helitron family. Our findings of the nonregular host-parasite interactions may be more conducive to the HT of transposons.

Electronic supplementary material

The online version of this article (10.1186/s13100-019-0165-4) contains supplementary material, which is available to authorized users.

A eukaryotic nicotinate-inducible gene cluster: convergent evolution in fungi and bacteria

Nicotinate degradation has hitherto been elucidated only in bacteria. In the ascomycete Aspergillus nidulans, six loci, hxnS/AN9178 encoding the molybdenum cofactor-containing nicotinate hydroxylase, AN11197 encoding a Cys2/His2 zinc finger regulator HxnR, together with AN11196/hxnZ, AN11188/hxnY, AN11189/hxnP and AN9177/hxnT, are clustered and stringently co-induced by a nicotinate derivative and subject to nitrogen metabolite repression mediated by the GATA factor AreA. These genes are strictly co-regulated by HxnR. Within the hxnR gene, constitutive mutations map in two discrete regions. Aspergillus nidulans is capable of using nicotinate and its oxidation products 6-hydroxynicotinic acid and 2,5-dihydroxypyridine as sole nitrogen sources in an HxnR-dependent way. HxnS is highly similar to HxA, the canonical xanthine dehydrogenase (XDH), and has originated by gene duplication, preceding the origin of the Pezizomycotina. This cluster is conserved with some variations throughout the Aspergillaceae. Our results imply that a fungal pathway has arisen independently from bacterial ones. Significantly, the neo-functionalization of XDH into nicotinate hydroxylase has occurred independently from analogous events in bacteria. This work describes for the first time a gene cluster involved in nicotinate catabolism in a eukaryote and has relevance for the formation and evolution of co-regulated primary metabolic gene clusters and the microbial degradation of N-heterocyclic compounds.

Somatic transposition and meiotically driven elimination of an active helitron family in Pleurotus ostreatus

Helitrons constitute a superfamily of DNA transposons that were discovered in silico and are widespread in most eukaryotic genomes. They are postulated to mobilize through a "rolling-circle" mechanism, but the experimental evidence of their transposition has been described only recently. Here, we present the inheritance patterns of HELPO1 and HELPO2 helitron families in meiotically derived progeny of the basidiomycete Pleurotus ostreatus. We found distorted segregation patterns of HELPO2 helitrons that led to a strong under-representation of these elements in the progeny. Further investigation of HELPO2 flanking sites showed that gene conversion may contribute to the elimination of such repetitive elements in meiosis, favouring the presence of HELPO2 vacant loci. In addition, the analysis of HELPO2 content in a reconstructed pedigree of subclones maintained under different culture conditions revealed an event of helitron somatic transposition. Additional analyses of genome and transcriptome data indicated that P. ostreatus carries active RNAi machinery that could be involved in the control of transposable element proliferation. Our results provide the first evidence of helitron mobilization in the fungal kingdom and highlight the interaction between genome defence mechanisms and invasive DNA.

Non-canonical Helitrons in Fusarium oxysporum

Background

Helitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. They occur widely in plants and animals, and have thus far been relatively little investigated in fungi.

Results

Here, we comprehensively survey Helitrons in several completely sequenced genomes representing the F. oxysporum species complex (FOSC). We thoroughly characterize 5 different Helitron subgroups and determine their impact on genome evolution and assembly in this species complex. FOSC Helitrons resemble members of the Helitron2 variant that includes Helentrons and DINEs. The fact that some Helitrons appeared to be still active in FOSC provided the opportunity to determine whether Helitrons occur as a circular intermediate in FOSC. We present experimental evidence suggesting that at least one Helitron subgroup occurs with joined ends, suggesting a circular intermediate. We extend our analyses to other Pezizomycotina and find that most fungal Helitrons we identified group phylogenetically with Helitron2 and probably have similar characteristics.

Conclusions

FOSC genomes harbour non-canonical Helitrons that are characterized by asymmetric terminal inverted repeats, show hallmarks of recent activity and likely transpose via a circular intermediate. Bioinformatic analyses indicate that they are representative of a large reservoir of fungal Helitrons that thus far has not been characterized.

Electronic supplementary material

The online version of this article (doi:10.1186/s13100-016-0083-7) contains supplementary material, which is available to authorized users.

Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates

Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.

Helitrons, the Eukaryotic Rolling-circle Transposable Elements

Helitrons, the eukaryotic rolling-circle transposable elements, are widespread but most prevalent among plant and animal genomes. Recent studies have identified three additional coding and structural variants of Helitrons called Helentrons, Proto-Helentron, and Helitron2. Helitrons and Helentrons make up a substantial fraction of many genomes where nonautonomous elements frequently outnumber the putative autonomous partner. This includes the previously ambiguously classified DINE-1-like repeats, which are highly abundant in Drosophila and many other animal genomes. The purpose of this review is to summarize what we have learned about Helitrons in the decade since their discovery. First, we describe the history of autonomous Helitrons, and their variants. Second, we explain the common coding features and difference in structure of canonical Helitrons versus the endonuclease-encoding Helentrons. Third, we review how Helitrons and Helentrons are classified and discuss why the system used for other transposable element families is not applicable. We also touch upon how genome-wide identification of candidate Helitrons is carried out and how to validate candidate Helitrons. We then shift our focus to a model of transposition and the report of an excision event. We discuss the different proposed models for the mechanism of gene capture. Finally, we will talk about where Helitrons are found, including discussions of vertical versus horizontal transfer, the propensity of Helitrons and Helentrons to capture and shuffle genes and how they impact the genome. We will end the review with a summary of open questions concerning the biology of this intriguing group of transposable elements.

VisualTE: a graphical interface for transposable element analysis at the genomic scale

Background

Transposable elements are mobile DNA repeat sequences, known to have high impact on genes, genome structure and evolution. This has stimulated broad interest in the detailed biological studies of transposable elements. Hence, we have developed an easy-to-use tool for the comparative analysis of the structural organization and functional relationships of transposable elements, to help understand their functional role in genomes.

Results

We named our new software VisualTE and describe it here. VisualTE is a JAVA stand-alone graphical interface that allows users to visualize and analyze all occurrences of transposable element families in annotated genomes. VisualTE reads and extracts transposable elements and genomic information from annotation and repeat data. Result analyses are displayed in several graphical panels that include location and distribution on the chromosome, the occurrence of transposable elements in the genome, their size distribution, and neighboring genes’ features and ontologies. With these hallmarks, VisualTE provides a convenient tool for studying transposable element copies and their functional relationships with genes, at the whole-genome scale, and in diverse organisms.

Conclusions

VisualTE graphical interface makes possible comparative analyses of transposable elements in any annotated sequence as well as structural organization and functional relationships between transposable elements and other genetic object. This tool is freely available at: http://lcb.cnrs-mrs.fr/spip.php?article867.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1351-5) contains supplementary material, which is available to authorized users.

Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi

BACKGROUND

Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleurotus ostreatus genomes using de novo detection and homology-based searching. We have analyzed the presence of helitron-captured genes as well as the expansion of helitron-specific helicases in fungi and performed a phylogenetic analysis of their conserved domains with other representative eukaryotic species.

RESULTS

Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes. Both putative autonomous and non-autonomous helitrons were transcriptionally active, and some of them carried highly expressed captured genes of unknown origin and function. In addition, both families contained eukaryotic, bacterial and viral domains within the helitron's boundaries. A phylogenetic reconstruction of RepHel helicases using the Helitron-like and PIF1-like helicase conserved domains revealed a polyphyletic origin for eukaryotic helitrons.

CONCLUSION

P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments. The occurrence of genes probably captured from other hosts inside the helitrons boundaries pose the hypothesis that an ancient horizontal transfer mechanism could have taken place. The viral domains found in some of these genes and the polyphyletic origin of RepHel helicases in the eukaryotic kingdom suggests that virus could have played a role in a putative lateral transfer of helitrons within the eukaryotic kingdom. The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.

Fungal biology in the post-genomic era

In this review I give a personal perspective of how fungal biology has changed since I started my Ph. D. in 1963. At that time we were working in the shadow of the birth of molecular biology as an autonomous and reductionistic discipline, embodied in Crick’s central dogma. This first period was methodologically characterised by the fact that we knew what genes were, but we could not access them directly. This radically changed in the 70s-80s when gene cloning, reverse genetics and DNA sequencing become possible. The “next generation” sequencing techniques have produced a further qualitative revolutionary change. The ready access to genomes and transcriptomes of any microbial organism allows old questions to be asked in a radically different way and new questions to be approached. I provide examples chosen somewhat arbitrarily to illustrate some of these changes, from applied aspects to fundamental problems such as the origin of fungal specific genes, the evolutionary history of genes clusters and the realisation of the pervasiveness of horizontal transmission. Finally, I address how the ready availability of genomes and transcriptomes could change the status of model organisms.

Rolling-circle transposons catalyze genomic innovation in a mammalian lineage

Rolling-circle transposons (Helitrons) are a newly discovered group of mobile DNA widespread in plant and invertebrate genomes but limited to the bat family Vespertilionidae among mammals. Little is known about the long-term impact of Helitron activity because the genomes where Helitron activity has been extensively studied are predominated by young families. Here, we report a comprehensive catalog of vetted Helitrons from the 7× Myotis lucifugus genome assembly. To estimate the timing of transposition, we scored presence/absence across related vespertilionid genome sequences with estimated divergence times. This analysis revealed that the Helibat family has been a persistent source of genomic innovation throughout the vespertilionid diversification from approximately 30–36 Ma to as recently as approximately 1.8–6 Ma. This is the first report of persistent Helitron transposition over an extended evolutionary timeframe. These findings illustrate that the pattern of Helitron activity is akin to the vertical persistence of LINE retrotransposons in primates and other mammalian lineages. Like retrotransposition in primates, rolling-circle transposition has generated lineage-specific variation and accounts for approximately 110 Mb, approximately 6% of the genome of M. lucifugus. The Helitrons carry a heterogeneous assortment of host sequence including retroposed messenger RNAs, retrotransposons, DNA transposons, as well as introns, exons and regulatory regions (promoters, 5′-untranslated regions [UTRs], and 3′-UTRs) of which some are evolving in a pattern suggestive of purifying selection. Evidence that Helitrons have contributed putative promoters, exons, splice sites, polyadenylation sites, and microRNA-binding sites to transcripts otherwise conserved across mammals is presented, and the implication of Helitron activity to innovation in these unique mammals is discussed.

UreA, the major urea/H+ symporter in Aspergillus nidulans

We report here the characterization of UreA, a high-affinity urea/H+ symporter of Aspergillus nidulans. The deletion of the encoding gene abolishes urea transport at low substrate concentrations, suggesting that in these conditions UreA is the sole transport system specific for urea in A. nidulans. The ureA gene is not inducible by urea or its precursors, but responds to nitrogen metabolite repression, necessitating for its expression the AreA GATA factor. In contrast to what was observed for other transporters in A. nidulans, repression by ammonium is also operative during the isotropic growth phase. The activity of UreA is down-regulated post-translationally by ammonium-promoted endocytosis. A number of homologues of UreA have been identified in A. nidulans and other Aspergilli, which cluster in four groups, two of which contain the urea transporters characterized so far in fungi and plants. This phylogeny may have arisen by gene duplication events, giving place to putative transport proteins that could have acquired novel, still unidentified functions.

Pervasive horizontal transfer of rolling-circle transposons among animals

Horizontal transfer (HT) of genes is known to be an important mechanism of genetic innovation, especially in prokaryotes. The impact of HT of transposable elements (TEs), however, has only recently begun to receive widespread attention and may be significant due to their mutagenic potential, inherent mobility, and abundance. Helitrons, also known as rolling-circle transposons, are a distinctive subclass of TE with a unique transposition mechanism. Here, we describe the first evidence for the repeated HT of four different families of Helitrons in an unprecedented array of organisms, including mammals, reptiles, fish, invertebrates, and insect viruses. The Helitrons present in these species have a patchy distribution and are closely related (80–98% sequence identity), despite the deep divergence times among hosts. Multiple lines of evidence indicate the extreme conservation of sequence identity is not due to selection, including the highly fragmented nature of the Helitrons identified and the lack of any signatures of selection at the nucleotide level. The presence of horizontally transferred Helitrons in insect viruses, in particular, suggests that this may represent a potential mechanism of transfer in some taxa. Unlike genes, Helitrons that have horizontally transferred into new host genomes can amplify, in some cases reaching up to several hundred copies and representing a substantial fraction of the genome. Because Helitrons are known to frequently capture and amplify gene fragments, HT of this unique group of DNA transposons could lead to horizontal gene transfer and incur dramatic shifts in the trajectory of genome evolution.

Phenotypes of mutations in the 5'-UTR of a limiting transcription factor in Aspergillus nidulans can be accounted for by translational inhibition and leaky scanning

The uaY gene encodes the transcriptional activator of purine catabolism genes in Aspergillus nidulans. uaY12 results in strongly defective growth on purines as nitrogen sources and in strongly diminished transcription of UaY-regulated genes. This mutation introduces an ATG codon 64 bp upstream of the uaY ATG, generating a 68-codon open reading frame (uORFA), overlapping with the uaY ORF. uaY12 revertants fall into three categories: i. The majority eliminate the aberrant ATG. The growth and transcriptional phenotypes of these revertants are identical to those of the wild type. i. Two revertants create a stop codon in frame with the uaY12 aberrant ATG, shortening the length of the uORFA, thus uORFA no longer overlaps the uaY ORF. The latter are partial suppressors of the uaY12 mutation, while chain termination suppressors, in turn, suppress this novel phenotype. iii. Two partial suppressors are unlinked to uaY. These two mutations result in a pleiotropic phenotype usually associated with ribosomal proteins. We hypothesize that uORFA strongly diminishes translation of the uaY ORF and that revertants negate this effect by a number of different mechanisms. The first-AUG rule and the phenomena of translational inhibition and leaky scanning provide a coherent explanation of the results presented in this article.

AgtA, the dicarboxylic amino acid transporter of Aspergillus nidulans, is concertedly down-regulated by exquisite sensitivity to nitrogen metabolite repression and ammonium-elicited endocytosis

We identified agtA, a gene that encodes the specific dicarboxylic amino acid transporter of Aspergillus nidulans. The deletion of the gene resulted in loss of utilization of aspartate as a nitrogen source and of aspartate uptake, while not completely abolishing glutamate utilization. Kinetic constants showed that AgtA is a high-affinity dicarboxylic amino acid transporter and are in agreement with those determined for a cognate transporter activity identified previously. The gene is extremely sensitive to nitrogen metabolite repression, depends on AreA for its expression, and is seemingly independent from specific induction. We showed that the localization of AgtA in the plasma membrane necessitates the ShrA protein and that an active process elicited by ammonium results in internalization and targeting of AgtA to the vacuole, followed by degradation. Thus, nitrogen metabolite repression and ammonium-promoted vacuolar degradation act in concert to downregulate dicarboxylic amino acid transport activity.

The 2008 update of the Aspergillus nidulans genome annotation: a community effort

The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology.

The nadA gene of Aspergillus nidulans, encoding adenine deaminase, is subject to a unique regulatory pattern

The adenine deaminase of A. nidulans, encoded by nadA, can be considered both as a catabolic and a purine salvage enzyme. We show that its transcriptional regulation reflects this double metabolic role. As all other genes involved in purine utilisation it is induced by uric acid, and this induction is mediated by the UaY transcription factor. However, it is also independently and synergistically induced by adenosine by a UaY-independent mechanism. At variance with all other enzymes of purine catabolism it is not repressed but induced by ammonium. This is at least partly due to the ammonium responsive GATA factor, AreA, acting in the nadA promoter as a competitor rather than in synergy with UaY. The adB gene, encoding adenylo-succinate synthetase, which can be considered both a biosynthetic and a salvage pathway enzyme, shares with nadA both ammonium and adenosine induction.

Helitrons on a roll: eukaryotic rolling-circle transposons

Rolling-circle eukaryotic transposons, known as Helitron transposons, were first discovered in plants (Arabidopsis thaliana and Oryza sativa) and in the nematode Caenorhabditis elegans. To date, Helitrons have been identified in a diverse range of species, from protists to mammals. They represent a major class of eukaryotic transposons and are fundamentally different from classical transposons in terms of their structure and mechanism of transposition. Helitrons seem to have a major role in the evolution of host genomes. They frequently capture diverse host genes, some of which can evolve into novel host genes or become essential for helitron transposition.

A tale of two dead ends: origin of a potential new gene and a potential new transposable element

An article in this issue of Molecular Microbiology by Cultrone et al. describes how a non-autonomous helitron element could arise from its autonomous parent transposon by deletion followed by readthrough into an adjacent gene and its promoter, thus providing a mechanism for distribution of a specifically regulated promoter sequence around the genome, where it would have the potential to evolve new functions.

Purification and characterization of the FeII- and alpha-ketoglutarate-dependent xanthine hydroxylase from Aspergillus nidulans

His6-tagged xanthine/alpha-ketoglutarate (alphaKG) dioxygenase (XanA) of Aspergillus nidulans was purified from both the fungal mycelium and recombinant Escherichia coli cells, and the properties of the two forms of the protein were compared. Evidence was obtained for both N- and O-linked glycosylation on the fungus-derived XanA, which aggregates into an apparent dodecamer, while bacterium-derived XanA is free of glycosylation and behaves as a monomer. Immunological methods identify phosphothreonine in both forms of XanA, with phosphoserine also detected in the bacterium-derived protein. Mass spectrometric analysis confirms glycosylation and phosphorylation of the fungus-derived sample, which also undergoes extensive truncation at its amino terminus. Despite the major differences in the properties of these proteins, their kinetic parameters are similar (kcat = 30-70 s-1, Km of alphaKG = 31-50 muM, Km of xanthine approximately 45 muM, and pH optima at 7.0-7.4). The enzyme exhibits no significant isotope effect when [8-2H]xanthine is used; however, it demonstrates a 2-fold solvent deuterium isotope effect. CuII and ZnII potently inhibit the FeII-specific enzyme, whereas CoII, MnII, and NiII are weaker inhibitors. NaCl decreases the kcat and increases the Km of both alphaKG and xanthine. The alphaKG cosubstrate can be substituted with alpha-ketoadipate (9-fold decrease in kcat and 5-fold increase in the Km compared to those of the normal alpha-keto acid), while the alphaKG analogue N-oxalylglycine is a competitive inhibitor (Ki = 0.12 muM). No alternative purines effectively substitute for xanthine as a substrate, and only one purine analogue (6,8-dihydroxypurine) results in significant inhibition. Quenching of the endogenous fluorescence of the two enzyme forms by xanthine, alphaKG, and DHP was used to characterize their binding properties. A XanA homology model was generated on the basis of the structure of the related enzyme TauD (PDB entry 1OS7) and provided insights into the sites of posttranslational modification and substrate binding. These studies represent the first biochemical characterization of purified xanthine/alphaKG dioxygenase.