Dating divergences in the Fungal Tree of Life: review and new analyses

Taylor, John W.; Berbee, Mary L.

doi:10.1080/15572536.2006.11832614

Cited by 303 publications

(297 citation statements)

References 35 publications

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“…S3A). Although several inversions occurred within syntenic blocks, the overall synteny can be traced before separation of the orders Eurotiales and Onygenales, dated between 150 and 400 Mya depending on molecular clock calibration (19). Members of other rvt lineages exhibit similar degrees of synteny ( Fig.…”

Section: Resultsmentioning

confidence: 93%

A widespread class of reverse transcriptase-related cellular genes

Gladyshev

Arkhipova

2011

Proc. Natl. Acad. Sci. U.S.A.

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Reverse transcriptases (RTs) polymerize DNA on RNA templates. They fall into several structurally related but distinct classes and form an assemblage of RT-like enzymes that, in addition to RTs, also includes certain viral RNA-dependent RNA polymerases (RdRP) synthesizing RNA on RNA templates. It is generally believed that most RT-like enzymes originate from retrotransposons or viruses and have no specific function in the host cell, with telomerases being the only notable exception. Here we report on the discovery and properties of a unique class of RT-related cellular genes collectively named rvt. We present evidence that rvts are not components of retrotransposons or viruses, but single-copy genes with a characteristic domain structure that may contain introns in evolutionarily conserved positions, occur in syntenic regions, and evolve under purifying selection. These genes can be found in all major taxonomic groups including protists, fungi, animals, plants, and even bacteria, although they exhibit patchy phylogenetic distribution in each kingdom. We also show that the RVT protein purified from one of its natural hosts, Neurospora crassa, exists in a multimeric form and has the ability to polymerize NTPs as well as dNTPs in vitro, with a strong preference for NTPs, using Mn 2+ as a cofactor. The existence of a previously unknown class of single-copy RT-related genes calls for reevaluation of the current views on evolution and functional roles of RNA-dependent polymerases in living cells.D NA-dependent polymerases are essential for cellular function, as they mediate the flow of genetic information from DNA to RNA to proteins (1). In contrast, RNA-dependent polymerases have long been associated with replication of selfish and parasitic genetic elements, such as viruses or transposons. Although the discovery of reverse transcriptase (RT) challenged the concept of unidirectionality of the flow of genetic information, this reverse direction has been reserved for retroviruses, pararetroviruses (hepadna-and caulimoviruses), and other RT-containing multicopy entities such as non-LTR and LTR retrotransposons, group II introns, retrons, and retroplasmids, as well as occasional retro (pseudo)genes (2-4). Similarly, viral RNA-dependent RNA polymerases (RdRPs), enzymes structurally related to RTs, serve to replicate the genomes of viruses that use RNA as genetic material (5). These and certain other polymerases are unified by the architecture known as "right hand," composed of the three subdomains called fingers, palm, and thumb (6). Like all polymerases, they use two-metal-ion catalysis for phosphoryl transfer reactions resulting in nucleotide addition.In 1997, this diverse superfamily of enzymes was joined by the telomerase reverse transcriptase (TERT), a specialized RT that maintains the ends of eukaryotic linear chromosomes by addition of short G-rich repeated DNA sequences that are copied multiple times via reverse transcription of a specific region of the associated RNA template constituting part of the holoenzyme (...

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Section: Resultsmentioning

confidence: 93%

A widespread class of reverse transcriptase-related cellular genes

Gladyshev

Arkhipova

2011

Proc. Natl. Acad. Sci. U.S.A.

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“…The phylogenetic position of U. virens was evaluated among other eleven selected fungal species (10 ascomycota and one basidiomycota outgroup) using a set of highly conserved singlecopy genes suggested for the Fungal Tree of Life 28 (Supplementary Table 10, Supplementary Note 5). The analysis revealed that U. virens is more closely related to two entomopathogenic Metarhizium spp.…”

Section: Resultsmentioning

confidence: 99%

Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics

et al. 2014

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Ustilaginoidea virens (Cooke) Takah is an ascomycetous fungus that causes rice false smut, a devastating emerging disease worldwide. Here we report a 39.4 Mb draft genome sequence of U. virens that encodes 8,426 predicted genes. The genome has B25% repetitive sequences that have been affected by repeat-induced point mutations. Evolutionarily, U. virens is close to the entomopathogenic Metarhizium spp., suggesting potential host jumping across kingdoms. U. virens possesses reduced gene inventories for polysaccharide degradation, nutrient uptake and secondary metabolism, which may result from adaptations to the specific floret infection and biotrophic lifestyles. Consistent with their potential roles in pathogenicity, genes for secreted proteins and secondary metabolism and the pathogen-host interaction database genes are highly enriched in the transcriptome during early infection. We further show that 18 candidate effectors can suppress plant hypersensitive responses. Together, our analyses offer new insights into molecular mechanisms of evolution, biotrophy and pathogenesis of U. virens.

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“…The phylogenetic distribution of mtTyrRSs with structural adaptations required for group I intron splicing activity in CYT-18 suggests that this activity was acquired by Pezizomycotina mtTyrRSs during or after the divergence of this fungal subphylum from Saccharomycotina, 350-600 million years ago (22). The driving force was presumably the need to compensate for structural defects acquired by group I introns that had inserted as mobile elements into essential mtDNA genes.…”

Section: Identification Of Functionally Important Amino Acids By Sequmentioning

confidence: 99%

Identification and evolution of fungal mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity

Paukstelis

Lambowitz

2008

Proc. Natl. Acad. Sci. U.S.A.

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The bifunctional Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) both aminoacylates mitochondrial tRNA Tyr and acts as a structure-stabilizing splicing cofactor for group I introns. Previous studies showed that CYT-18 has distinct tRNA Tyr and group I intron-binding sites, with the latter formed by three small ''insertions'' in the nucleotide-binding fold and other structural adaptations compared with nonsplicing bacterial tyrosyl-tRNA synthetases. Here, analysis of genomic sequences shows that mitochondrial tyrosyl-tRNA synthetases with structural adaptations similar to CYT-18's are uniquely characteristic of fungi belonging to the subphylum Pezizomycotina, and biochemical assays confirm group I intron splicing activity for the enzymes from several of these organisms, including Aspergillus nidulans and the human pathogens Coccidioides posadasii and Histoplasma capsulatum. By combining multiple sequence alignments with a previously determined cocrystal structure of a CYT-18/group I intron RNA complex, we identify conserved features of the Pezizomycotina enzymes related to group I intron and tRNA interactions. Our results suggest that mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity evolved during or after the divergence of the fungal subphyla Pezizomycotina and Saccharomycotina by a mechanism involving the concerted differentiation of preexisting protein loop regions. The unique group I intron splicing activity of these fungal enzymes may provide a new target for antifungal drugs.aminoacyl-tRNA synthetase ͉ medical mycology ͉ ribozyme ͉ RNA splicing ͉ protein structure function T he Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (mtTyrRS; CYT-18 protein) is one of a number of proteins that adapted to function in splicing autocatalytic group I and group II introns in different organisms (1-3). One class of these proteins, splicing factors, functions by binding specifically to the intron RNAs and stabilizing their catalytically active RNA structure for efficient splicing in vivo. Groups I and II intron splicing factors differ among organisms and are commonly host proteins that have or had some other functions. Most promote the splicing of only one or a small number of structurally related introns, but CYT-18 is an exception, because it is able to splice diverse group I introns from N. crassa and other organisms (4-6). The idiosyncratic nature of group I and II intron splicing factors suggests that they adapted to function in splicing relatively recently in evolution, after the dispersal of the introns as mobile elements (2, 3).The CYT-18 protein was identified genetically in a screen for splicing-deficient mutants and shown to function in splicing three group I introns in N. crassa mitochondria: the mitochondrial (mt) large subunit rRNA (mtLSU) intron, ND1-I1, and cob-I2 (7,8). Biochemical studies showed that purified recombinant CYT-18 by itself stimulates group I intron splicing in vitro, that it recognizes conserved secondary and tertiary structure f...

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Dating divergences in the Fungal Tree of Life: review and new analyses

Cited by 303 publications

References 35 publications

A widespread class of reverse transcriptase-related cellular genes

A widespread class of reverse transcriptase-related cellular genes

Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics

Identification and evolution of fungal mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity

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