scholarly journals High nucleotide substitution rates associated with retrotransposon proliferation drive dynamic secretome evolution in smut pathogens

2021 ◽  
Author(s):  
JRL Depotter ◽  
B Ökmen ◽  
MK Ebert ◽  
J Beckers ◽  
J Kruse ◽  
...  
Keyword(s):  
Mating Type ◽  
Substitution Rate ◽  
Nucleotide Substitution ◽  
Long Terminal Repeat Retrotransposons ◽  
Nucleotide Substitution Rate ◽  
Type Locus ◽  
Genome Expansion ◽  
Long Reads ◽  
Genes Encoding ◽  
Flanking Regions

AbstractTransposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to long terminal repeat retrotransposons (LTR-RTs) of the Copia and Gypsy superfamilies. From the studied smuts, LTR-RTs proliferated the most recently and to the furthest extent in the U. hordei genome, in which they make up for 19.5% of the genome. Interestingly, the extent of TE proliferation in different smut species is positively correlated to the mating-type locus size, which is largest in U. hordei with up to ~560 kb. TE transposition within the mating-type loci and their flanking regions are mating-type specific, which is likely due to the very low recombination activity in this region. Furthermore, LTR-RT proliferation was found to be associated with higher nucleotide substitution levels, as genes in genome regions that are rich in dynamic LTR-RTs display higher nucleotide substitution levels. The high nucleotide substitution rate particularly affected the evolution of genes encoding secreted proteins as substitutions more frequently led to amino acid alterations. The mechanism behind this increase in nucleotide substitution rate remains elusive, but seems not to be a consequence of the repeat-induced point mutation (RIP) mechanism, as genes and LTR-RTs did not display typical RIP substitutions.

scholarly journals Genomic diversity of SARS-CoV-2 can be accelerated by a mutation in the nsp14 gene

2020 ◽  
Author(s):  
Kosuke Takada ◽  
Mahoko Takahashi Ueda ◽  
Tokiko Watanabe ◽  
So Nakagawa
Keyword(s):  
Amino Acid ◽  
Substitution Rate ◽  
Nucleotide Substitution ◽  
Acid Sites ◽  
Genomic Diversity ◽  
Nucleotide Substitution Rate ◽  
Structural Protein ◽  
Wild Type ◽  
Gamma Delta ◽  
Evolutionarily Conserved

AbstractNucleotide substitution rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is relatively low compared to the other RNA viruses because coronaviruses including SARS-CoV-2 encode non-structural protein 14 (nsp14) that is an error-correcting exonuclease protein. In this study, to understand genome evolution of SARS-CoV-2 in the current pandemic, we examined mutations of SARS-CoV-2 nsp14 which could inhibit its error-correcting function. First, to obtain functionally important sites of nsp14, we examined 62 representative coronaviruses belonging to alpha, beta, gamma, delta, and unclassified coronaviruses. As a result, 99 out of 527 amino acid sites of nsp14 were evolutionarily conserved. We then examined nsp14 sequences obtained from 28,082 SARS-CoV-2 genomes and identified 6 amino acid changes in nsp14 mutants that were not detected in the 62 representative coronaviruses. We examined genome substitution rates of these mutants and found that an nsp14 mutant with a proline to leucine change at position 203 (P203L) showed a higher substitution rate (35.9 substitutions/year) than SARS-CoV-2 possessing wild-type nsp14 (19.8 substitutions/year). We confirmed that the substitution rate of the P203L is significantly higher than those of other variants containing mutations in structural proteins. Although the number of SARS-CoV-2 variants containing P203L mutation of nsp14 is limited (26), these mutants appeared at least 10 times independently in the current pandemic. These results indicated that the molecular function of nsp14 is important for survival of various coronaviruses including SARS-CoV-2 and that some mutations such as P203L of nsp14 inhibiting its error-correcting function are removed rapidly due to their deleterious effects.

scholarly journals Mating-Type-Specific and Nonspecific PAK Kinases Play Shared and Divergent Roles in Cryptococcus neoformans

2002 ◽  
Vol 1 (2) ◽  
pp. 257-272 ◽  
Author(s):  
Ping Wang ◽  
Connie B. Nichols ◽  
Klaus B. Lengeler ◽  
Maria E. Cardenas ◽  
Gary M. Cox ◽  
...  
Keyword(s):  
Cryptococcus Neoformans ◽  
Mating Type ◽  
Fungal Pathogen ◽  
Sexual Cycle ◽  
Type Locus ◽  
Serotype A ◽  
A Cells ◽  
Genes Encoding ◽  
Opportunistic Fungal Pathogen ◽  
Synthetically Lethal

ABSTRACT Cryptococcus neoformans is an opportunistic fungal pathogen with a defined sexual cycle involving fusion of haploid MATα and MATa cells. Virulence has been linked to the mating type, and MATα cells are more virulent than congenic MATa cells. To study the link between the mating type and virulence, we functionally analyzed three genes encoding homologs of the p21-activated protein kinase family: STE20α, STE20a, and PAK1. In contrast to the STE20 genes that were previously shown to be in the mating-type locus, the PAK1 gene is unlinked to the mating type. The STE20α, STE20a, and PAK1 genes were disrupted in serotype A and D strains of C. neoformans, revealing central but distinct roles in mating, differentiation, cytokinesis, and virulence. ste20α pak1 and ste20a pak1 double mutants were synthetically lethal, indicating that these related kinases share an essential function. In summary, our studies identify an association between the STE20α gene, the MATα locus, and virulence in a serotype A clinical isolate and provide evidence that PAK kinases function in a MAP kinase signaling cascade controlling the mating, differentiation, and virulence of this fungal pathogen.

Changes in Mate Recognition Through Alterations of Pheromones and Receptors in the Multisexual Mushroom FungusSchizophyllum commune

Genetics ◽  
2001 ◽  
Vol 158 (4) ◽  
pp. 1491-1503 ◽  
Author(s):  
Thomas J Fowler ◽  
Michael F Mitton ◽  
Lisa J Vaillancourt ◽  
Carlene A Raper
Keyword(s):  
Amino Acid ◽  
Mating Type ◽  
Schizophyllum Commune ◽  
Mate Recognition ◽  
Mating Types ◽  
Loss Of Function ◽  
Sequence Comparisons ◽  
Type Locus ◽  
Step Model ◽  
Genes Encoding

AbstractSchizophyllum commune has thousands of mating types defined in part by numerous lipopeptide pheromones and their G-protein-coupled receptors. These molecules are encoded within multiple versions of two redundantly functioning B mating-type loci, Bα and Bβ. Compatible combinations of pheromones and receptors, produced by individuals of different B mating types, trigger a pathway of fertilization required for sexual development. Analysis of the Bβ2 mating-type locus revealed a large cluster of genes encoding a single pheromone receptor and eight different pheromones. Phenotypic effects of mutations within these genes indicated that small changes in both types of molecules could significantly alter their specificity of interaction. For example, a conservative amino acid substitution in a pheromone resulted in a gain of function toward one receptor and a loss of function with another. A two-amino-acid deletion from a receptor precluded the mutant pheromone from activating the mutant receptor, yet this receptor was activated by other pheromones. Sequence comparisons provided clues toward understanding how so many variants of these multigenic loci could have evolved through duplication and mutational divergence. A three-step model for the origin of new variants comparable to those found in nature is presented.

scholarly journals Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12106
Author(s):  
Mikhail I. Schelkunov ◽  
Maxim S. Nuraliev ◽  
Maria D. Logacheva
Keyword(s):  
Substitution Rate ◽  
Nucleotide Substitution ◽  
Nucleotide Substitution Rate ◽  
Genomic Comparison ◽  
Plant Family ◽  
Plastid Genomes ◽  
The Family ◽  
Unknown Reason ◽  
Order Of Magnitude ◽  
Insight Into

The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.

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