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RNA-directed silencing mechanisms play important roles in the regulation of eukaryotic gene expression. In plants, insects, nematodes and fungi RNA silencing mechanisms are also involved in innate antiviral defence responses.
To counter antiviral
RNA silencing, viruses from plants, insects and fungi encode RNA silencing suppressors (RSSs). Recent studies suggest that RNA silencing in mammals, or RNA interference (
RNAi), is also involved in antiviral responses. In particular, there is increasing evidence that cellular regulatory
microRNAs (miRNAs) have a function in restricting virus replication in mammalian cells. Similar to plant and insect viruses, several mammalian viruses encode RSS factors that inhibit the RNAi mechanism. Several of these suppressors are multifunctional proteins that were previously shown to block innate antiviral immune responses involving the interferon (IFN) pathway.
Further reading:
Labels: MicroRNAs, miRNA, RNA silencing suppressors, RNAi, RSSs
New nucleic acid stabilization technologies may allow for the storage of DNA and RNA at room temperature in a cost-effective, environmentally friendly manner.
A recent study evaluates two novel products for room temperature DNA storage: Biomatrica's DNA SampleMatrix technology and GenVault's GenTegra DNA technology. The study compares the integrity and quality of DNA stored using these products against DNA stored in a freezer by performing downstream testing with short range PCR, long range PCR, DNA sequencing, and SNP microarrays. In addition, the investigators tested Biomatrica's RNAstable product for its ability to preserve RNA at room temperature for use in a quantitative reverse transcription PCR assay.
from Wan et al
in Green Technologies for Room Temperature Nucleic Acid StorageFurther reading:
Green Technologies for Room Temperature Nucleic Acid StorageLabels: Biomatrica, DNA SampleMatrix, DNA technology, GenTegra, GenVault, Storage of DNA
The parasexual cycle was discovered and then developed as a genetic system in
Aspergillus nidulans (=
Emericella nidulans) during the 1950s. Although discovered in a teleomorphic species, the parasexual soon became an important alternative to sex for doing genetics in anamorphic aspergilli. During the decades before recombinant DNA approaches became available, the parasexual cycle was exploited to recombine genetic markers in such economically important anamorphic species as
A. flavus, A. fumigatus, and
A. niger. During the 1950s and 1960s, fungal geneticists developed
A. nidulans into a highly sophisticated model for genetics, joining
Neurospora crassa as a premier system for providing elegant mechanistic insights on recombination and other aspects of eukaryotic biology. Carbon and nitrogen repression, pH regulation, polar growth, signal transduction, hyphal morphogenesis and the cell cycle were all fundamental research areas that were significantly advanced using
A. nidulans as a model. To give but one example, gamma tubulin was discovered using blocked mitotic mutants of
A. nidulans.
Suggested reading: Mycology PublicationsSome of the most interesting biochemistry carried out by
Aspergillus and other filamentous fungi has not been amenable to traditional genetic analysis. The elegant genetics available to model fungi such as
Aspergillus nidulans and
Neurospora crassa was not an option for the study of 'non-model' species such as
A. flavus and
A. oryzae, even with application of the parasexual cycle and recombinant DNA approaches. For this reason genomics promises a radical improvement for gaining a new level of understanding about the genetics and the theoretical protein coding genes of these anamorphic organisms. The genomic revolution has been brought about by improved methodologies for sequencing, generating libraries, annotation and so forth. After DNA sequencing, automated annotation uses bioinformatic gene finding programmes to locate the protein coding regions of genomes. These programmes work best when 'trained' on the appropriate genome. Automated annotation can provide a good first draft of the gene content and arrangement of a genome. Nevertheless, automatic annotation is notoriously imprecise and therefore must be subject to continuous revisions as more experimentally based information becomes available. After annotation, deduced genes can be classified as enzymes, receptors, transcription factors and so forth. Annotated genomes allow us to compare genes descended from the same ancestor across many different organisms. Sometimes this comparative genomic approach allows us to assign putative functions to unknown predicted genes.
Suggested reading: Genomics and Molecular BiologyThe simultaneous publication of three
Aspergillus genome manuscripts in
Nature in December 2005 established
Aspergillus as the leading filamentous fungal genus for comparative genomic studies. Like most major genome projects, these
Aspergillus efforts were collaborations between a large sequencing centre and the respective community of scientists. For example, the Institute for Genome Research (TIGR) worked with the
Aspergillus fumigatus community.
A. nidulans was sequenced at the Broad Institute.
A. oryzae was sequenced in Japan at the National Institute of Advanced Industrial Science and Technology. The Joint Genome Institute ( JGI) of the Department of Energy has released sequence date for a citric acid-producing strain of
A. niger. TIGR, now re-named the Venter Institute is currently spear-heading a project on the
A. flavus genome.
Genome sizes for sequenced species of
Aspergillus range from approximately 29.3 Mb for
A. fumigatus to 37.1 Mb for
A. oryzae while the numbers of predicted genes vary from approximately 9926 for
A. fumigatus to approximately 12,071 for
A. oryzae. The genome size of an enzyme producing strain of
A. niger is of intermediate size at 33.9 Mb.
Aspergillus species are only one group among a large number of eukaryotes now catalogued in databanks. There are currently well over 100 fungal genome projects in various stages of completion. In addition to full-fledged genome projects, various EST (expressed sequence tag) projects identify expressed genes by sequencing cDNA copies of mRNA. This approach provides a 'poor man's' strategy for genomics and provides valuable information about the coding regions of a genome expressed under different environmental conditions. ESTs also guide later annotation of full genomes. Furthermore,
DNA microarrays are available for an increasing number of
Aspergillus genomes and their use allows targeted functional analyses.
Our expectations for genome projects have become higher than they were just a few years ago. It is no longer enough to determine the DNA sequence and catalogue the predicted genes. Now we hope to become genomic detectives using sequence similarities to find new enzymes, secondary metabolites and other biologically important gene products. There is a high expectation that such 'genomic mining' will uncover new natural products and other interesting discoveries.
Comparative genomics is a growing field in its own right. Using molecular sequence alignment, evolutionary relationships can be inferred. For example, one of the most salient finding coming out of the
A. flavus genome project is its close sequence similarity and genomic architecture to that of
A. oryzae genome. Since visible phenotype is a manifestation of many genes and pathways acting together, the high genomic identity merely confirms what taxonomists have known since they first described the
A. flavus-oryzae group of yellow-green aspergilli. The morphological, physiological and genomic correspondence between the species is all the more remarkable because of their differing economic repercussions in human society.
A. flavus produces aflatoxin and is a pan-kingdom pathogen capable of causing serious disease in plants, insects and vertebrates.
A. oryzae is both non-toxigenic and non-pathogenic and is widely used in human food and beverage preparations.
DNA data permit us to make strong inferences about the comparative biology of these and other
Aspergillus species so as to reconstruct possible scenarios for the evolution of mating types, secondary metabolite clusters, enzymes involved in biomass degradation and other important pathways. Comparative genomics data can be leveraged to characterize biosynthetic processes. Using micro arrays and proteomics technology, we can study expression levels. Together with advanced bioinformatics and data analysis tools, we are gaining new insights into the functional properties and activities of
Aspergillus fungal genomes. However, many important questions remain unanswered. Large numbers of deduced genes still cannot be assigned to functional classes. Our ability to acquire genome-wide data has not enlightened us about the mechanics of pathogenicity and competitiveness, and at the broadest ecological level we are still a long way from understanding why some species are common whereas others are rare.
It is becoming clear that the 'easy' part of the research has been obtaining the DNA sequence. Interpreting these sequences and understanding the ways in which DNA sequences direct metabolism are much more complex undertakings than many molecular biologists predicted. Experimental characterization and functional analysis remain the rate limiting steps in translating genomics data into the drug discovery pipeline as well as for harnessing other aspects of
Aspergillus metabolism. Nevertheless, opportunities for exploiting genomic data are already apparent. New ways to connect traditional biology, gene function and evolution are on the horizon.
Aspergillus species remain resilient models for studying basic questions in eukaryotic biology. Undoubtedly,
Aspergillus genomics will enlighten fundamental insights into cell biology as well as have important implications for agriculture, industry and medicine.
Suggested reading: Aspergillus: Molecular Biology and Genomics Adapted from
An Overview of the Genus Aspergillus by
Joan W. Bennett writing in
Aspergillus: Molecular Biology and GenomicsFurther readingLabels: A. fumigatus, A. niger, Aspergillus, Aspergillus nidulans, Emericella nidulans, gamma tubulin, Neurospora crassa