A homozygous duplication of the FGG exon 8-intron 8 junction causes congenital afibrinogenemia. Lessons learned from the study of a large consanguineous Turkish family

Congenital afibrinogenemia is the most severe congenital fibrinogen disorder, characterised by undetectable fibrinogen in circulation. Causative mutations can be divided into two main classes: null mutations with no protein production at all and missense mutations producing abnormal protein chains that are retained inside the cell. The vast majority of cases are due to single base pair mutations or small insertions or deletions in the coding regions or intron-exon junctions of FGB, FGA and FGG. Only a few large rearrangements have been described, all deletions involving FGA. Here we report the characterization of a 403 bp duplication of the FGG exon 8-intron 8 junction accounting for congenital afibrinogenemia in a large consanguineous family from Turkey. This mutation, which had escaped detection by Sanger sequencing of short PCR amplicons of coding sequences and splice sites, was identified by studying multiple alignments of reads obtained from Whole Exome Sequencing of a heterozygous individual followed by PCR amplification and sequencing of a larger portion of FGG. Because the mutation duplicates the donor splice site of intron 8, we predicted that the impact of the mutation would be on FGG transcript splicing. Analysis of mRNAs produced by cells transiently transfected with normal or mutant minigene constructs showed that the duplication causes production of several aberrant FGG transcripts generating premature truncating codons.

Bi-allelic loss of ERGIC1 causes relatively mild arthrogryposis

Arthrogryposis describes the presence of multiple joint-contractures. Clinical severity of this phenotype is variable, and more than 400 causative genes have been proposed. Among these, ERGIC1 is a recently reported candidate encoding a putative transmembrane protein of the ER-Golgi interface. Two homozygous missense variants have been reported in patients with relatively mild non-syndromic arthrogryposis. In a consanguineous family with two affected siblings presenting congenital arthrogryposis and some facial dysmorphism we performed prenatal array-CGH, postnatal targeted exome and genome sequencing. Genome sequencing identified a homozygous 22.6 Kb deletion encompassing the promoter and first exon of ERGIC1. mRNA quantification showed the complete absence of ERGIC1 expression in the two affected siblings and a decrease in heterozygous parents. Our observations validate the pathogenic role of ERGIC1 in congenital arthrogryposis and demonstrate that complete loss of function causes a relatively mild phenotype. These findings will contribute to improve genetic counseling of ERGIC1 mutations.

Rapid genotypic change and plasticity in arbuscular mycorrhizal fungi is caused by a host shift and enhanced by segregation

Arbuscular mycorrhizal fungi (AMF) are among the most abundant symbionts of plants, improving plant productivity and diversity. They are thought to mostly grow vegetatively, a trait assumed to limit adaptability. However, AMF can also harbor genetically different nuclei (nucleotypes). It has been shown that one AMF can produce genotypically novel offspring with proportions of different nucleotypes. We hypothesized that (1) AMF respond rapidly to a change of environment (plant host) through changes in the frequency of nucleotypes; (2) genotypically novel offspring exhibit different genetic responses to environmental change than the parent; and (3) genotypically novel offspring exhibit a wide range of phenotypic plasticity to a change of environment. We subjected AMF parents and offspring to a host shift. We observed rapid and large genotypic changes in all AMF lines that were not random. Genotypic and phenotypic responses were different among offspring and their parents. Even though growing vegetatively, AMF offspring display a broad range of genotypic and phenotypic changes in response to host shift. We conclude that AMF have the ability to rapidly produce variable progeny, increasing their probability to produce offspring with different fitness than their parents and, consequently, their potential adaptability to new environmental conditions. Such genotypic and phenotypic flexibility could be a fast alternative to sexual reproduction and is likely to be a key to the ecological success of AMF.

Heat-inducible RNAi for gene functional analysis in plants

Controlling gene expression during plant development is an efficient method to explore gene function and RNA interference (RNAi) is now considered as a powerful technology for gene functional analysis. However, constitutive gene silencing cannot be used with genes involved in fundamental processes such as embryo viability or plant growth and alternative silencing strategies avoiding these limitations should be preferred. Tissue-specific and inducible promoters, able to control gene expression at spatial and/or temporal level, can be used to circumvent viability problems. In this chapter, after a rapid overview of the inducible promoters currently used for transgenic approaches in plants, we describe a method we have developed to study gene function by heat-inducible RNAi. This system is easy to use and complementary to those based on chemical gene inducer treatments and might be useful for both research and biotechnological applications.

Competitive ability not kinship affects growth of Arabidopsis thaliana accessions

In many organisms, individuals behave more altruistically towards relatives than towards unrelated individuals. Here, we conducted a study to determine if the performance of Arabidopsis thaliana is influenced by whether individuals are in competition with kin or non-kin. We selected seven pairs of genetically distinct accessions that originated from local populations throughout Europe. We measured the biomass of one focal plant surrounded by six kin or non-kin neighbours in in vitro growth experiments and counted the number of siliques produced per pot by one focal plant surrounded by four kin or non-kin neighbours. The biomass and number of siliques of a focal plant were not affected by the relatedness of the neighbour. Depending on the accession, a plant performed better or worse in a pure stand than when surrounded by non-kin plants. In addition, whole-genome microarray analyses revealed that there were no genes differentially expressed between kin and non-kin conditions. In conclusion, our study does not provide any evidence for a differential response to kin vs non-kin in A. thaliana. Rather, the outcome of the interaction between kin and non-kin seems to depend on the strength of the competitive abilities of the accessions.

Gene silencing using a heat-inducible RNAi system in Arabidopsis

Controlling gene expression during plant development is an efficient tool to explore gene function. In this paper, we describe a gene expression system driven by a heat-shock gene promoter (HSP18.2), to trigger the expression of an intron-containing inverted-repeat. RNA interference became a powerful way for gene functional analysis by reverse genetic approaches. However, constitutive gene silencing cannot be used with genes involved in fundamental processes such as embryo viability. Inducible promoters provide an alternative approach for temporal and spatial gene expression control and we described here a new system, complementary to those using chemical gene inducers. To evaluate the efficiency of this system, RNA corresponding to the phytoene desaturase gene of Arabidopsis thaliana was used as a reporter gene in transgenic plants and a comparative study was performed using either the CaMV35S constitutive promoter or the HSP18.2 inducible promoter.

Seed germination is blocked in Arabidopsis putative vacuolar sorting receptor (atbp80) antisense transformants

The membrane receptor protein from pea, peabp80, has been shown to function by in vitro binding studies, and in vivo in yeast mutant, as a vacuolar sorting receptor (VSR). Families of proteins with homology to peabp80 have been identified in many plants including Arabidopsis: The family of membrane receptors, atbp80a-f (Arabidopsis thaliana binding protein 80 kDa) is highly homologous to peabp80 and may also function as vacuolar sorting receptors. Interactions with vacuolar sorting determinants have been shown only in vitro for atbp80b. In this paper, atbp80b was over- and under-expressed in Arabidopsis. Transgenic plants that over-expressed atbp80b showed no visible phenotype. However, antisense transformants were defective in germination. In non-germinating antisense transformants the embryo appeared to be normal, but, using several methods, it was not possible to rescue the non-germinating seeds, indicating that the mechanisms were probably independent of a seed-coat-imposed inhibition. To make a correlation between the lack of germination and gene expression, transcription analysis of all atbp80 genes was performed in the non-germinating antisense seeds indicating that all the normally transcribed genes were not detected. Then, a gene expression study of atbp80s genes was carried-out following seed imbibition and in various organs during wild-type plant development showing that all the genes from the family were transcribed and differentially expressed.

Systemic mycosis caused by a new Cladophialophora species

A 22-year-old woman suffered from haemoptyses of unknown aetiology. A tumour in the lingula was diagnosed histologically to be a granulomatosis, most likely a sarcoidosis. Two years later, the patient returned with dyspnoea caused by a granulomatous tumour in the trachea, histologically similar to that seen earlier. After bronchoscopic laser resection, cortisone therapy was applied but without success. A fungus was subsequently discovered histologically and was cultivated from biopsy specimens. Retrospective research of primary histological slides led to the conclusion that a mycosis was the initial cause of the tumours. The mycosis was successfully treated with high-dose itraconazole for 1 year, combined with 5-fluorocytosine (5-FC) during the first few months. The causative agent was found to be a new species of Cladophialophora, and is described as C. arxii Tintelnot; its key characteristics are presented.

Nutritional physiology and taxonomy of human-pathogenic Cladosporium-Xylohypha species

Physiological profiles of type, authentic and some additional isolates of Cladosporium-Xylohypha species of purported herpotrichiellaceous relationship are established. This group comprises melanized catenate hyphomycetes which are prevalently found on the human host. The species are excluded from the genus Cladosporium and are classified in the genus Cladophialophora. Taeniolella boppii is also transferred to this genus. Cladosporium bantianum (= Xylohypha emmonsii) and C. trichoides are considered conspecific and are now referred to as Cladophialophora bantiana. Meso-erythritol, L-arabinitol, ethanol and growth at 40 degrees C are found to be the most useful criteria for species distinction. The species Cladosporium carrionii is found to be heterogeneous. The anamorph of the saprophytic ascomycete Capronia pilosella is morphologically similar to an authentic strain of Cladosporium carrionii, but physiologically distinct. A diagnostic key for the recognized Cladophialophora species and to morphologically similar taxa is provided.

Phylogenetic relationships of human-pathogenic Cladosporium (Xylohypha) species inferred from partial LS rRNA sequences

The controversy about the appropriate taxonomic placement of agents of subcutaneous and systemic mycoses in either Cladosporium or Xylohypha, both genera characterized by conidia being produced in dry, acropetal chains, was addressed with partial sequencing of LS ribosomal RNA. Observation of catenate anamorphs in species of Capronia (Ascomycotina, Herpotrichiellaceae), a genus which also has anamorphs in Exophiala, suggested the possibility of a close interrelationship of all human-associated taxa. To test this hypothesis, partial sequences of 43 strains of Cladosporium/Xylohypha were analysed. Human-pathogenic and saprophytic Cladosporium species were found to be phylogenetically distinct from each other and, on the basis of known teleomorph relationships, were considered to be anamorphs of Herpotrichiellaceae and Mycosphaerellaceae, respectively. They should therefore be classified in different anamorph-genera; Cladosporium being restricted to plant-associated species. A relatively large proportion of the Herpotrichiellaceae is presumed to be animal-associated. The black yeast genus Exophiala was also confirmed to be of herpotrichiellaceous relationship. The genus Xylohypha is unrelated.