Regulation of low-molecular weight organic acid production in fungi

Organic acids produced by fungi have been proposed to have many roles in wood-decay processes, lignocellulose degradation or plant pathogenesis involving saprotrophic or pathogenic fungi, as well as in nutrient acquisition and metal detoxification involving mycorrhizal or rhizosphere-inhabiting fungi. In comparison with other fungi, a considerable body of work has been devoted to the comprehension of biosynthesis pathways in fungi involved in industrial production of organic acids, and also in those involved in wood-decay processes and pathogenicity. In this review we therefore focus on information available from these different types of low-molecular weight organic acid (LMWOA) producing fungi in order to better understand the environmental cues involved in regulating production of LMWOAs.     

丛枝菌根养分吸收和转运机制的研究历史与进展

丛枝菌根真菌(AMF)在土壤生态系统中分布最广且在农业生态系统中作用最大,是颇受研究人员关注的一类菌根真菌。多年来,人们尝试着用各种技术和方法从不同角度、不同层次对AMF与植物的互惠机制进行研究并取得了较大进展。近年来分子技术在该领域得以广泛应用,使得人们对这一共生体的互惠机制有了更为详尽的了解。从营养学角度入手,综述了国内外关于丛枝菌根(AM)真菌对土壤中养分吸收和转运机制的研究进展,并在概括当前AMF促生机制研究热点的基础上对其发展前景作了展望。     

Hypogeous sequestrate fungi in South America – how well do we know them?

Collecting and studying hypogeous sequestrate fungi and their particular fruiting biology has always been challenging and intriguing for scientists. However, knowledge of hypogeous taxa has for a long time been limited mainly to the Northern Hemisphere, and more recently, Australia. Nevertheless, cumulative information on sequestrate fungi for South America (SA) has increased considerably over the years, and constitutes by itself, the aim of this review. We have reviewed the available published literature, from 1880 until recent times, to extract information on records, ecology, and morphological characteristics of hypogeous sequestrate fungi from SA. Based on the 172 taxa cited in the available literature, a trend of increasing interest in the study of these fungi in the region is apparent, yet with an uneven distribution among countries, climate belts, and nature of forest habitats. Hypogeous truffle-like species in SA play a key role in regulating nutrient and carbon cycles and in all ecosystem multifunctionality. The symbiotic status is provided for most species listed, and mutualism, especially ectomycorrhizal, is predominant (82 %). The hypogeous sequestrate fungi in SA are an understudied group of fungi, with exceptional anatomical and biological features as well as in many cases intriguing phylogenetic relationships, requiring more attention and analysis from mycologists.     

The homeobox genes of <Emphasis Type="Italic">Encephalitozoon cuniculi</Emphasis> (Microsporidia) reveal a putative mating-type locus

Homeobox genes have been found in animals, fungi, and plants. Recently, the complete genomic sequence of Encephalitozoon cuniculi has become available and it was shown that this Microsporida species is related to fungi. Given this close relatedness to fungi, I have searched the genome of E. cuniculifor homeobox genes. There are 12 homeobox genes as well as one STE12 orthologue. The large number of homeobox genes when compared to the annotations, which only list one, suggests that possibly other smaller genes may have been overlooked in the published analysis and E. cuniculi may have more than 1,997 genes. Sequence and phylogenetic analyses show that the E. cuniculi homeobox genes also fall into two distinct groups, with two TALE and ten typical homeobox genes being present. Like in the mating-type locus of yeast and other fungi, one TALE and one typical homeobox are found in close proximity of each other on the chromosome, suggesting that Microsporidia also contain a mating-type locus.     

Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes

Background  

Genes responsible for biosynthesis of fungal secondary metabolites are usually tightly clustered in the genome and co-regulated with metabolite production. Epipolythiodioxopiperazines (ETPs) are a class of secondary metabolite toxins produced by disparate ascomycete fungi and implicated in several animal and plant diseases. Gene clusters responsible for their production have previously been defined in only two fungi. Fungal genome sequence data have been surveyed for the presence of putative ETP clusters and cluster data have been generated from several fungal taxa where genome sequences are not available. Phylogenetic analysis of cluster genes has been used to investigate the assembly and heredity of these gene clusters.     

Progress towards implementing the Biodiversity Action Plan for stipitate hydnoid fungi in Scotland

Summary

Stipitate hydnoid (‘tooth’) fungi are considered to be threatened throughout much of central and northern Europe. In response to concern about the status of these fungi in the UK, a Biodiversity Action Plan has been developed for 14 species in this group. As a first step towards implementation of this plan, a number of surveys have been initiated, to determine the current status and distribution of hydnoid fungi. An overview of the results of these surveys is described. A series of distribution maps are presented, based on a compilation of early records and the results of a recent field survey in Scottish coniferous forests. The difficulties of interpreting early records are discussed, with particular reference to the taxonomie confusion that has surrounded this group of fungi. Although available data provide little evidence for decline of hydnoid fungi, a number of species display very restricted distributions within Scotland. The recent discovery of several species new to Britain emphasises the need for further field surveys to define the current status of these fungi with greater accuracy.     

Mycoheterotrophic interactions are not limited to a narrow phylogenetic range of arbuscular mycorrhizal fungi

The majority of achlorophyllous mycoheterotrophic plant species associate with arbuscular mycorrhizal fungi (AMF). Previous studies have shown that some species are highly specialized towards narrow lineages of AMF and have suggested that only particular lineages of these fungi are targeted by mycoheterotrophic plants. To test this hypothesis, we analyzed all available partial SSU sequences of AMF associated with mycoheterotrophic plants including data from 13 additional specimens from French Guiana, Gabon and Australia. Sequences were assigned to 'virtual taxa' (VT) according to the MaarjAM database. We found that 20% of all known Glomeromycota VT are involved in mycoheterotrophic interactions and the majority of associations involve Glomeraceae (Glomus Group A) fungi. While some mycoheterotrophic plant species have been found growing with only a single VT, many species are able to associate with a wide range of AMF. We calculated significant phylogenetic clustering of Glomeromycota VT involved in mycoheterotrophic interactions, suggesting that associations between mycoheterotrophic plants and AMF are influenced by the phylogenetic relationships of the fungi. Our results demonstrate that many lineages of AMF are prone to exploitation by mycoheterotrophic plants. However, mycoheterotrophs from different plant lineages and different geographical regions tend to be dependent on lineages of AMF that are phylogenetically related.     

Use of pH auxostats to grow filamentous fungi in continuous flow culture at maximum specific growth rate

Abstract The pH auxostat employs a pH-derived feedback control of biomass concentration and allows continuous flow cultures of organisms to be grown at their maximum specific growth rate. We examine three modifications of the pH auxostat system for the growth of filamentous fungi and discuss the suitability of each method according to the biomass concentration desired, the medium used and the equipment available. Fusarium graminearum and Geotrichum candidum were used for this work and it was possible to maintain steady state pH auxostats of these filamentous fungi for up to 20 days. pH auxostats have not previously been described for filamentous fungi.     

Cloning and characterization of the isopenicillin N synthetase gene mediating the formation of the beta-lactam ring in Aspergillus nidulans

Genomic clones containing an Aspergillus nidulans isopenicillin N synthetase (IPNS) gene have been identified by heterologous hybridization with a Cephalosporium acremonium DNA probe. The open reading frame encodes a 331 amino acid polypeptide with extensive homology with the genes of other beta-lactam-producing fungi. The gene product has been overexpressed in Escherichia coli and shown to have activity of IPNS. This represents the first evidence at the molecular level that the biosynthesis of penicillins in A. nidulans occurs by the same pathway as in other beta-lactam-producing microorganisms. Comparison of available nucleotide sequences from IPNS genes suggests a horizontal transmission of the gene between the prokaryotic beta-lactam producers of the genus Streptomyces and the filamentous fungi.     

Genetic Manipulations in Dermatophytes

Dermatophytes are a group of closely related fungi that nourish on keratinized materials for their survival. They infect stratum corneum, nails, and hair of human and animals, accounting the largest portion of fungi causing superficial mycoses. Huge populations are suffering from dermatophytoses, though the biology of these fungi is largely unknown yet. Reasons are partially attributed to the poor amenability of dermatophytes to genetic manipulation. However, advancements in this field over the last decade made it possible to conduct genetic studies to satisfying extents. These included genetic transformation methods, indispensable molecular tools, i.e., dominant selectable markers, inducible promoter, and marker recycling system, along with improving homologous recombination frequency and gene silencing. Furthermore, annotated genome sequences of several dermatophytic species have recently been available, ensuring an optimal recruitment of the molecular tools to expand our knowledge on these fungi. In conclusion, the establishment of basic molecular tools and the availability of genomic data will open a new era that might change our understanding on the biology and pathogenicity of this fungal group.     

Of patterns and pathways: microarray technologies for the analysis of filamentous fungi

During recent years, microarrays have been firmly established as valuable tools for the discovery of novel biological phenomena. Especially in combination with whole genome sequences, microarray data can help unravel the dynamics of the expressed genome. For filamentous fungi, microarray studies have already been performed with more than 20 different species; these investigations have explored a variety of different aspects of fungal biology. In this review, I will give an overview of some of the key questions that have been addressed using microarray hybridizations with filamentous fungi, with particular focus on the analysis of co-regulated pathways and physically clustered genes, as well as on the use of microarray data to determine a molecular phenotype. Additionally, a number of useful, freely available software tools for the analysis of fungal microarray data will be discussed.     

Synthesis of potential buprenorphine intermediates by selective microbial <Emphasis Type="Italic">N</Emphasis>- and <Emphasis Type="Italic">O</Emphasis>-demethylation

A group of filamentous fungi from the genus Cunninghamella have been identified as potential biocatalysts in the generation of potential buprenorphine intermediates. A simple batch fermentation procedure results in the formation of dealkylated alkaloid compounds that are readily available for analysis and further chemical modification.     

Endophytic fungi as novel sources of biopesticides: the Macaronesian Laurel forest,a case study

Endophytes fungi have been widely bioprospected to find new drugs and drug leads including antimicrobial agents and antifungals. However, an important role in host plant protection has been suggested for their presence and their metabolites. Therefore, nematicidal and insecticidal effects of their metabolites should be expected. In this review, the literature data available on insecicidal and nematicidal compounds identified from fungal endophytes are presented. Additionally we present a recent study on the endophytic biodiversity of a unique paleoflora, the Macaronesian laurel forest, in the light of their role in plant protection.     

The role of VAM fungi in nitrogen dynamics in maize-bean intercrops

Nitrogen (N) transfer from N-fixing legumes via vesicular-arbuscular mycorrhizal (VAM) fungi to associated non-fixing plants has been demonstrated in greenhouse experiments. To date, this transfer has been shown only where mineral N is applied shortly before harvest, and hence is readily available. We have yet to demonstrate VAM-mediated N transfer where soil-N is limiting, a condition under which most traditional legume-nonlegume intercrops are grown.In this study, ¹⁵N-enriched soil (with 0.28%N) was used to distinguish between the uptake of soil- and atmospherically-derived N in maize grown with beans in the presence or absence of VAM fungi. VAM infection did not result in transfer of fixed N or soil N from bean to maize, despite a VAM-stimulated increase in N fixation in bean. In fact, beans were more competitive for soil N when mycorrhizal. N content in beans increased by 75% with a concomitant 22% decrease in mg N per maize plant. The competitive effect may have resulted from a VAM-mediated shift in carbon allocation in beans (but not maize) from shoots to roots.     

Genetic engineering of filamentous fungi--progress, obstacles and future trends

Filamentous fungi are widely used in biotechnology as cell factories for the production of chemicals, pharmaceuticals and enzymes. In order to improve their productivities, genetic engineering strategies can be powerful approaches. Different transformation techniques as well as DNA- and RNA-based methods to rationally design metabolic fluxes have been developed for industrially important filamentous fungi. However, the lack of efficient genetic engineering approaches still forms an obstacle for a multitude of fungi producing new and commercially interesting metabolites. This review summarises the variety of options that have recently become available to introduce and control gene expression in filamentous fungi and discusses their advantages and disadvantages. Furthermore, important considerations that have to be taken into account to design the best engineering strategy will be discussed.     

Aquaporins in yeasts and filamentous fungi

Recently, genome sequences from different fungi have become available. This information reveals that yeasts and filamentous fungi possess up to five aquaporins. Functional analyses have mainly been performed in budding yeast, Saccharomyces cerevisiae, which has two orthodox aquaporins and two aquaglyceroporins. Whereas Aqy1 is a spore-specific water channel, Aqy2 is only expressed in proliferating cells and controlled by osmotic signals. Fungal aquaglyceroporins often have long, poorly conserved terminal extensions and differ in the otherwise highly conserved NPA motifs, being NPX and NXA respectively. Three subgroups can be distinguished. Fps1-like proteins seem to be restricted to yeasts. Fps1, the osmogated glycerol export channel in S. cerevisiae, plays a central role in osmoregulation and determination of intracellular glycerol levels. Sequences important for gating have been identified within its termini. Another type of aquaglyceroporin, resembling S. cerevisiae Yfl054, has a long N-terminal extension and its physiological role is currently unknown. The third group of aquaglyceroporins, only found in filamentous fungi, have extensions of variable size. Taken together, yeasts and filamentous fungi are a fruitful resource to study the function, evolution, role and regulation of aquaporins, and the possibility to compare orthologous sequences from a large number of different organisms facilitates functional and structural studies.     

Microbial acid-stable α-amylases: Characteristics,genetic engineering and applications

Among the wide variety of amylolytic enzymes synthesized by microorganisms, α-amylases are the most widely used biocatalysts in starch saccharification, baking industries and textile desizing. These enzymes randomly cleave the α-1,4-glycosidic linkages in starch, generating maltose and malto-oligosaccharides. The commercially available α-amylases have certain limitations, such as limited activity at low pH and Ca²⁺-dependence, and therefore, the search for novel acid-stable and thermostable amylases from extremophilic microorganisms and the engineering of the already available enzymes have been the major areas of research in this field over the years. Several attempts have been made to find suitable microbial sources of acid-stable and thermostable α-amylases. Acid-stable α-amylases have been reported in fungi, bacteria and archaea. α-Amylases that are active at elevated temperatures have been reported in bacteria as well as in archaea. α-Amylases that possess both characteristics, to the extent required for their various applications are very scarce. The developments that have been made in molecular biology, directed evolution and structural conformation studies of α-amylases for improving their properties to suit various industrial applications are discussed in this review.     

Nature and bioactivities of endolichenic fungi in Pseudocyphellaria sp., Parmotrema sp. and Usnea sp. at Hakgala montane forest in Sri Lanka

Aim:  The aim of this study was to investigate the nature and bioactivities of endolichenic fungi in three abundant lichens, Pseudocyphellaria sp., Usnea sp. and Parmotrema sp. in the lower elevation of Hakgala montane forest in Sri Lanka.
Methods and Results:  Endolichenic fungal strains, fungi that live asymptomatically in the lichen thallus, much the same way as endophytic fungi live within healthy plant tissues, were isolated from three abundant lichen species, Pseudocyphellaria sp., Usnea sp. and Parmotrema sp., at Hakgala montane forest in Sri Lanka, using the surface sterilization method. Nine endolichenic fungal strains were isolated from Parmotrema sp. and Usnea sp. separately, while 11 endolichenic fungi were recovered from the lichen Pseudocyphellaria sp. Isolation of endolichenic fungus Chrysosporium sp. 2 was common to all three lichen species. Substrate utilization patterns and antifungal activities of eight endolichenic fungal species were evaluated and the results revealed that all the test fungi were able to produce at least one enzyme to utilize the test substrates. Nigrospora sp., Chrysosporium sp. 1 and 2 and Cladosporium sp. showed antifungal activities on growth of some selected plant pathogenic fungi.
Conclusions:  Endolichenic fungal strains (29) were isolated from the lichens Parmotrema sp., Usnea sp. and Pseudocyphellaria sp. in Sri Lanka. Chrysosporium sp. 2 was common in all three lichens. Some of these endolichenic fungal strains showed antifungal activities against common plant pathogenic fungi and they are capable of utilizing the substrates by producing specific enzymes.
Significance and Impact of the Study:  The diversity and prevalence of the endolichenic fungi have not been studied extensively and this is the first report of isolation and identification of endolichenic fungi in lichens available in Sri Lanka.     

Interactions between aboveground herbivores and the mycorrhizal mutualists of plants

Plant growth, reproduction and survival can be affected both by mycorrhizal fungi and aboveground herbivores, but few studies have examined the interactive effects of these factors on plants. Most of the available data suggest that severe herbivory reduces root colonization by vesicular-arbuscular and ectomycorrhizal fungi. However, the reverse interaction has also been documented - mycorrhizal fungi deter herbivores and interact with fungal endophytes to influence herbivory. Although consistent patterns and mechanistic explanations are yet to emerge, it is likely that aboveground herbivore-mycorrhiza interactions have important implications for plant populations and communities.