White rot, in fallen trees, on forest floor, degrades lignin
Sources: www.genomenewsnetwork.org,www.ebi.ac.uk/genomes/index.html,www.genomesonline.org, and Kellis et al. (2003, 2004).
Sources: www.genomenewsnetwork.org,www.ebi.ac.uk/genomes/index.html,www.genomesonline.org, and Kellis et al. (2003, 2004).
or white rot fungus, which is found commonly on dead trees and wood fragments on the forest floor. To date, white rot fungus is the only basidomycete (mushroom-forming fungus) that has had its genome sequenced (Martinez et al. 2004). White rot owes its name to the fact that the fungus 'bleaches' wood by degrading the (brown-coloured) lignin, rendering the white cellulose visible. Lignin forms protective sheaths around cellulose fibrils in plant cell walls. The biodegradation of lignin by white rot is supported by unique extracellular oxidative enzymes (peroxidases and oxidases) that act non-specifically via the generation of free radicals attacking the lignin molecule. There are many other ecologically important fungi commonly found on dead organic material that contribute to processing of organic matter and cycling of nutrients in natural ecosystems (Aspergillus, Trichoderma, Cladosporium, Morteriella), but their genomes have yet to be sequenced.
The genome sizes of fungi are between those of bacteria and higher eukaryotes. Neurospora crassa, a mycelium-forming fungus, has one of the largest fungal genomes sequenced so far (Galagan et al. 2003). Comparing this genome with S. cerevisiae, Braun et al. (2000) suggested that the relatively small genome of baker's yeast is due to a process of 'streamlining' by loss of genes. Detailed comparisons of S. cerevisiae with the filamentous fungus Ashbya gossypii (Dietrich et al. 2004) and the unicellular Kluyveromyces waltii (Kellis et al. 2004) have confirmed that the evolution of S. cerevisiae has included a whole-genome duplication, followed by extensive rearrangements and loss of genes. These conclusions are in accordance with the idea that unicellularity in fungi is an apomorphic condition and that yeasts evolved independently several times from multicellular ancestors, not the other way around.
N. crassa (orange bread mould) has been a famous model organism for genetic and biochemical studies since the classical experiments of Beadle and Tatum in 1942, who proved that for every enzyme there is one gene (the one gene/one enzyme hypothesis). Although Neurospora is an ascomycete like S. cerevisiae, it is more similar to animals than to yeast in several ways. For example, unlike yeast but like mammals, it has a clearly discernable circadian rhythm, it methylates DNA to control gene expression, and it has complex I in the respiratory chain. With all this biochemical research, Neurospora is the best-characterized of the filamentous fungi, but its ecology remains relatively unexplored. Being moderately thermophilic, Neurospora was thought to occur mainly in moist tropical and subtropical regions, but recent surveys have also found Neurospora colonizing trees and shrubs killed by wildfires in temperate regions (Jacobson et al. 2004; Fig. 3.16). Mycological inventories showed that in North America isolates
were comprised predominantly of a single species, Neurospora discreta, but in southern Europe species collected included N. crassa, N. discreta, Neurospora sitophila, and Neurospora tetrasperma.
The life cycle of S. cerevisiae is of the diplobiontic type; that is, it cycles through two distinct phases, one diploid and one haploid (Fig. 3.17). The dip-loid stage grows vegetatively by budding off new cells and forming colonies. Under certain conditions, such as deprivation of carbon or nitrogen, it can form stress-resistant ascospores. Exactly how sporulation is triggered is currently under investigation. Ascospores are of two types, called a and a. They sit together in the ascus and upon germination produce two so-called mating types. These haploid cells can grow vegetatively by budding, a property that provides unique opportunities to geneticists, because the expression of traits in this stage is not confounded by dominance: the phenotype is a direct result of the genotype. The two haploid mating types may interact with each other by means of hormones, which induce a characteristic change in shape, leading to pear-shaped cells, called shmoos after the lovable creatures in Li'l Abner's comic strip from 1948. The process of sexual conjugation can occur only between opposite mating types. It involves a complicated series of cell-surface changes to facilitate fusion and is mediated by the hormones in a manner that is mating-type specific. The life cycle of N. crassa is similar, except that the diploid vegetative stage is suppressed and the zygote proceeds directly to form an ascus.
SGDtm is the Saccharomyces Genome Database (www.yeastgenome.org) where information about the molecular biology and genetics of baker's yeast is filed and presented to the world. The database includes a variety of search options that allow one to consult the genome sequence; analysis tools such as BLAST (see Section 2.4), programs for homology searches, and information about protein structure, as well as contact details for more than 1000 people in the yeast research community. The database also provides a list of recently published papers on all aspects of yeast molecular biology and links to databases of the other fungi listed in
Table 3.4. The organizational principles of the database are discussed by Dwight et al. (2004). Over the years the SGD has seen a dramatic increase in its usage, and has served as a template for other databases. The success of SGD, as measured by the numbers of pages viewed, user responses, and number of downloads, is due in large part to the network philosophy that has guided its mission and organization since it was established in 1993. The yeast genome was the first for which microarrays were developed (see Section 2.2). An oligonucleotide microarray (Affymetrix Yeast Genome 2.0 Array) is available that contains 10 765 probes, allowing one to address almost all genes of both S. cerevisiae and Schizosaccharomyces pombe at the same time.
A series of in-depth comparative genomic studies has recently been conducted in which the genome of S. cerevisiae was compared with other fungi in and outside of the order Sacchar-omycetales (Brachat et al. 2003; Cliften et al. 2003; Kellis et al. 2003, 2004; Dietrich et al. 2004; Dujon et al. 2004). An important argument for sequencing species that have a known phylogenetic relationship with S. cerevisiae is that it could help in the identification of genes and regulatory elements in the genome of S. cerevisiae. The idea is that ortho-logous sequences need to show a considerable degree of conservation before an ORF is considered a gene. True protein-encoding genes will typically be under selective pressure and show conservation, whereas ORFs that are not expressed will show mutations that are different for each species. When this approach is applied to regulatory elements it is called phylogenetic footprint-ing, referring to the fact that regulatory elements tend to be conserved across widely distant species and are recognizable in the genome as 'footprints' (Cliften et al. 2003). Comparative genomics applied to closely related rather than distant species has been called phylogenetic shadowing; this approach was first applied to sequences from 17 different primates as 'shadows' of the human genome (Bofelli et al. 2003).
As an example of a comparative genomics study in yeast, let us consider the work by Kellis et al. (2003). This author analysed the relationship among orthologous genes using a reading frame conservation test. This test classifies each ORF in S. cerevisiae as biologically meaningful or meaningless, depending on the proportion of the sequence over which conservation with other species is observed. Each of the other species was considered a 'voter', 'approving' or 'rejecting' the sequence in S. cerevisiae. Obviously, the procedure carries a risk that true genes under strong selective pressure in one of the species are rejected as biologically meaningful, but this was prevented by looking in detail at each rejection. Confidence in the method was increased when it appeared that only a few already annotated ORFs were rejected as genes. Inspection showed that in all of these possibly false-negative cases the annotated ORFs were indeed likely to be spurious. The analysis of Kellis et al. (2003) pruned the yeast gene catalogue of 503 genes, leaving only 20 ORFs in the database unresolved and decreasing the number of protein-encoding genes with more than 100 amino acids to 5538 (see also Table 2.1).
Further insight into the S. cerevisae genome has recently been obtained from comparisons with more distantly related species. Dujon et al. (2004) sequenced four species from the hemiascomycete group, Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, and Yarrowia lipolytica, and compared their genomes with that of S. cerevisae. A total of approximately 24200 novel genes was identified, and their translation products were classified into about 4700 families. Pairwise comparisons were made between the species to establish the degree of sequence divergence between orthologous genes. It appeared that the five yeast species together spanned a genetic diversity comparable to the entire phylum Chordata. For example, the average sequence identity between orthologous genes (translated into proteins) between S. cerevisiae and C. glabrata was 65%, between S. cerevisiae and K. lactis 60%, and between S. cerevisiae and Y. lipolytica 49%. This is less than the average sequence identity of proteins between mouse and fugu fish (70%) and comparable to that found between the urochordate sea squirt, Ciona intestinalis, and the mammals! The lesson of this large-scale comparative genomics study was that the evolutionary distance between yeasts, despite their very similar morphology, is extremely large.
Although molecular biologists have developed the habit (to the amusement of zoologists) of calling the nematode C. elegans a worm, the animal has nothing to do with the true worms, the Annelida, since it is classified in a completely separate phylum, Nematoda. Phylogenomic analysis has demonstrated that this phylum is related to the arthropods and belongs to the so-called moulting animals, the Ecdysozoa (Dopazo and Dopazo 2005); the annelids are classified with the molluscs in another superphylum, Lophotrochozoa.
C. elegans is one of the rhabditid nematodes, a group of tiny, free-living, bacteria-feeding animals, living in soils, dead organic material, or wherever there are bacteria. On the basis of rRNA gene sequences, 17 species are classified in the genus Caenorhabditis, including C. briggsae, the other nematode whose genome has been sequenced completely. Classification of nematodes is complicated by the fact that the external structure of the animals is not very diversified. The morphology of the most important diagnostic characters, the mouthparts, and other aspects of external morphology do not always fit with the molecular data and therefore the names assigned to higher-order categories in the classical taxonomy are sometimes illogical when arranging the species according to a molecular phylogeny. For example, the order Rhabditida does not indicate a monophyletic group, but appears to fall into at least two different phylogenetic lineages (see http://nematol.unh. edu/phylogeny.php, and Blaxter et al. 1998).
Despite their morphological uniformity, the phylum Nematoda is extremely diverse from a genetic point of view. Analysing a large collection of ESTs (>250000) from 30 different nematode species, Parkinson et al. (2004) found that 30-50% of the transcriptome of each species was unique to that species. Consequently, a single nematode like C. elegans can reveal only a small fraction of the genomic diversity of even its own phylum. A phylogeny of 53 species of nematodes, based on small-subunit rRNA sequences, is given in Fig. 3.18 (Blaxter et al. 1998). The figure also provides information on feeding habits, which diverge widely within the nematodes as a whole; one can find bacteriovores (like C. elegans), fungi-vores, predators, omnivores, plant parasites, and animal parasites. Fig. 3.18 shows that there is no phylogenetic conservation of feeding habits; feeding modes are scattered throughout the tree. The great biodiversity of feeding habits, life-history patterns, and colonizing capacity makes the Nematoda a very suitable group for community bioindication. When each species is given a score on a scale of colonizers to persisters, the weighted sum of these scores for a given community (the maturity index) can be used as a indicator of habitat quality (Bongers and Ferris 1999).
The phylum Nematoda includes many parasites, such as the well-known intestinal roundworm of pigs, Ascaris lumbricoides, the small human pin-worm Enterobius vermicularis, which infects 30-80% of schoolchildren in western countries, and various species causing serious diseases in tropical countries, such as Onchocerca volvulus, the causative agent of river blindness (onchocerciasis), which is spread by the bite of an infected blackfly. Experiments have shown that the inflammatory response in the human eye causing blindness, which is triggered by the presence of dying nematode microfilariae, is not only due to the worm itself, but also to toxins excreted by an endosymbiotic Wolbachia bacterium (Saint Andre et al. 2002). The genome of this Wolbachia is currently being sequenced. So the genomic studies on C. elegans have important ramifications for parasite research (Blaxter et al. 1998) and scientific networks are currently in development that address the field of nematode parasitomics: for example, the Filarial Genome Network (www.nematodes.org/fgn/ pnb/filbio.html), named after one of the parasitic species in the onchocercid group, Filaria martis. Although the interest in parasite genomics is exclusively medical at the moment, parasites are important agents in the population dynamics of many wild species and progress in the medical sector could well have a future spin-off to ecology. There are also several nematodes that form cysts
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