scholarly journals RNA Silencing Gene Truncation in the Filamentous Fungus Aspergillus nidulans

2007 ◽  
Vol 7 (2) ◽  
pp. 339-349 ◽  
Author(s):  
T. M. Hammond ◽  
J. W. Bok ◽  
M. D. Andrewski ◽  
Y. Reyes-Domínguez ◽  
C. Scazzocchio ◽  
...  
Keyword(s):  
Aspergillus Nidulans ◽  
Rna Silencing ◽  
Biological Function ◽  
Population Analysis ◽  
Species Level ◽  
Model Species ◽  
Closely Related Species ◽  
The Core ◽  
Filamentous Ascomycete ◽  
Ascomycete Fungi

ABSTRACT The genus Aspergillus is ideally suited for the investigation of RNA silencing evolution because it includes species that have experienced a variety of RNA silencing gene changes. Our work on this subject begins here with the model species Aspergillus nidulans. Filamentous ascomycete fungi generally each encode two of the core RNA silencing proteins, Dicer and Argonaute, but A. nidulans appears to have lost one of each to gene truncation events. Although a role in growth, development, or RNA silencing was not detected for the truncated genes, they do produce spliced and poly(A)-tailed transcripts, suggesting that they may have an undetermined biological function. Population analysis demonstrates that the truncated genes are fixed at the species level and that their full-length orthologs in a closely related species are also unstable. With these gene truncation events, A. nidulans encodes only a single intact Dicer and Argonaute. Their deletion results in morphologically and reproductively normal strains that are incapable of experimental RNA silencing. Thus, our results suggest that the remaining A. nidulans RNA silencing genes have a “nonhousekeeping” function, such as defense against viruses and transposons.

scholarly journals Doing it alone: Unisexual reproduction in filamentous ascomycete fungi

2021 ◽  
Vol 35 ◽  
pp. 1-13
Author(s):  
Andi M. Wilson ◽  
Raphael Gabriel ◽  
Steven W. Singer ◽  
Timo Schuerg ◽  
P. Markus Wilken ◽  
...  
Keyword(s):  
Filamentous Ascomycete ◽  
Unisexual Reproduction ◽  
Ascomycete Fungi

scholarly journals Unique N-Terminal Interactions Connect F-BOX STRESS INDUCED (FBS) Proteins to a WD40 Repeat-like Protein Pathway in Arabidopsis

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2228
Author(s):  
Edgar Sepulveda-Garcia ◽  
Elena C. Fulton ◽  
Emily V. Parlan ◽  
Lily E. O’Connor ◽  
Anneke A. Fleming ◽  
...  
Keyword(s):  
Environmental Stress ◽  
Biological Function ◽  
Interacting Proteins ◽  
Wd40 Repeat ◽  
Protein Targets ◽  
Scf Complex ◽  
Protein Target ◽  
The Core ◽  
N Terminus ◽  
Nuclear Events

SCF-type E3 ubiquitin ligases provide specificity to numerous selective protein degradation events in plants, including those that enable survival under environmental stress. SCF complexes use F-box (FBX) proteins as interchangeable substrate adaptors to recruit protein targets for ubiquitylation. FBX proteins almost universally have structure with two domains: A conserved N-terminal F-box domain interacts with a SKP protein and connects the FBX protein to the core SCF complex, while a C-terminal domain interacts with the protein target and facilitates recruitment. The F-BOX STRESS INDUCED (FBS) subfamily of plant FBX proteins has an atypical structure, however, with a centrally located F-box domain and additional conserved regions at both the N- and C-termini. FBS proteins have been linked to environmental stress networks, but no ubiquitylation target(s) or biological function has been established for this subfamily. We have identified two WD40 repeat-like proteins in Arabidopsis that are highly conserved in plants and interact with FBS proteins, which we have named FBS INTERACTING PROTEINs (FBIPs). FBIPs interact exclusively with the N-terminus of FBS proteins, and this interaction occurs in the nucleus. FBS1 destabilizes FBIP1, consistent with FBIPs being ubiquitylation targets SCFFBS1 complexes. This work indicates that FBS proteins may function in stress-responsive nuclear events, and it identifies two WD40 repeat-like proteins as new tools with which to probe how an atypical SCF complex, SCFFBS, functions via FBX protein N-terminal interaction events.

scholarly journals Unique Patterns of Mating Pheromone Presence and Absence could Result in the Ambiguous Sexual Behaviours of Colletotrichum Species

2020 ◽  
Author(s):  
Andrea Melissa Wilson ◽  
RV Lelwala ◽  
PWJ Taylor ◽  
MJ Wingfield ◽  
BD WINGFIELD
Keyword(s):  
Mating Type ◽  
Molecular Mechanisms ◽  
Mating Strategies ◽  
Mating Partner ◽  
Filamentous Ascomycete ◽  
Sexual Behaviours ◽  
History Of ◽  
Ascomycete Fungi ◽  
Presence And Absence ◽  
Sexual Progeny

Abstract Background: Colletotrichum species are known to engage in unique sexual behaviours that differ significantly from the mating strategies of other filamentous ascomycete species. Most ascomycete fungi require the expression of both the MAT1-1-1 and MAT1-2-1 genes to regulate mating type and induce sexual reproduction. In contrast, all isolates of Colletotrichum are known to harbour only the MAT1-2-1 gene and yet, are capable of recognizing suitable mating partners and producing sexual progeny. The molecular mechanisms contributing to mating types and behaviours in Colletotrichum are thus unknown. Results: A comparative genomics approach analysing genomes from 47 Colletotrichum isolates was used to elucidate a putative molecular mechanism underlying the unique sexual behaviours observed in Colletotrichum species. The existence of only the MAT1-2 idiomorph was confirmed across all species included in this study. Comparisons at the loci harbouring the two mating pheromones and their cognate receptors revealed interesting patterns of gene presence and absence as well as gene loss. The results also showed that these genes have been lost multiple times over the evolutionary history of this genus. Conclusion: The multiple losses of the pheromone genes in these species suggest strong selection against the typical mating strategies seen in other species. This further suggests that these pheromones no longer play a role in mating type determination and that the species of this genus have undiscovered mechanisms by which to control mating type and mating partner recognition. This research thus provides a base from which further interrogation of this topic can take place.

scholarly journals Colobopsis explodens sp. n., model species for studies on “exploding ants” (Hymenoptera, Formicidae), with biological notes and first illustrations of males of the Colobopsis cylindrica group

ZooKeys ◽  
2018 ◽  
Vol 751 ◽  
pp. 1-40 ◽  
Author(s):  
Alice Laciny ◽  
Herbert Zettel ◽  
Alexey Kopchinskiy ◽  
Carina Pretzer ◽  
Anna Pal ◽  
...  
Keyword(s):  
Species Complex ◽  
Mandibular Gland ◽  
Species Group ◽  
The Philippines ◽  
Species Level ◽  
Model Species ◽  
Species Identity ◽  
Taxonomic Description ◽  
Biological Studies ◽  
Taxonomic Changes

A taxonomic description of all castes of Colobopsisexplodens Laciny & Zettel, sp. n. from Borneo, Thailand, and Malaysia is provided, which serves as a model species for biological studies on “exploding ants” in Southeast Asia. The new species is a member of the Colobopsiscylindrica (COCY) group and falls into a species complex that has been repeatedly summarized under the name Colobopsissaundersi (Emery, 1889) (formerly Camponotussaundersi). The COCY species group is known under its vernacular name “exploding ants” for a unique behaviour: during territorial combat, workers of some species sacrifice themselves by rupturing their gaster and releasing sticky and irritant contents of their hypertrophied mandibular gland reservoirs to kill or repel rivals. This study includes first illustrations and morphometric characterizations of males of the COCY group: Colobopsisexplodens Laciny & Zettel, sp. n. and Colobopsisbadia (Smith, 1857). Characters of male genitalia and external morphology are compared with other selected taxa of Camponotini. Preliminary notes on the biology of C.explodens Laciny & Zettel, sp. n. are provided. To fix the species identity of the closely related C.badia, a lectotype from Singapore is designated. The following taxonomic changes within the C.saundersi complex are proposed: Colobopsissolenobia (Menozzi, 1926), syn. n. and Colobopsistrieterica (Menozzi, 1926), syn. n. are synonymized with Colobopsiscorallina Roger, 1863, a common endemic species of the Philippines. Colobopsissaginata Stitz, 1925, stat. n., hitherto a subspecies of C.badia, is raised to species level.

scholarly journals The ant genus Tetramorium Mayr (Hymenoptera: Formicidae) in the Malagasy region—taxonomy of the T. bessonii, T. bonibony, T. dysalum, T. marginatum, T. tsingy, and T. weitzeckeri species groups

Zootaxa ◽  
2012 ◽  
Vol 3365 (1) ◽  
pp. 1 ◽  
Author(s):  
FRANCISCO HITA GARCIA ◽  
BRIAN L. FISHER
Keyword(s):  
New Species ◽  
Single Species ◽  
Species Level ◽  
The Other ◽  
Current Status ◽  
Species Status ◽  
The Core ◽  
Core Species ◽  
Species Groups ◽  
Level Identification

The taxonomy of the T. bessonii, T. bonibony, T. dysalum, T. marginatum, T. tsingy, and T. weitzeckeri species groups isrevised. A total of 33 species is treated, of which 27 are newly described and one is raised to species status. The T.weitzeckeri group contains the single species T. humbloti Forel, which is of Afrotropical origin and the only representativeof the group in the Malagasy region. The species T. bessonii Forel, T. dysalum Bolton, T. marginatum Forel, and T. stein-heili Forel, which were originally members of the T. weitzeckeri group, are now placed in other groups. Tetramorium bes-sonii is the core species of the T. bessonii group, which also contains the four newly described species T. artemis sp. n., T.malagasy sp. n., T. ryanphelanae sp. n., T. wardi sp. n., and T. orientale Forel stat. n., which was a junior synonym of T.bessonii but is now raised to species rank. The T. dysalum group is a moderately-sized group with ten species, of whichonly T. dysalum and T. steinheili were previously known; the other eight species are all newly described. The newly described species in this group are: T. ambatovy sp. n., T. macki sp. n., T. mallenseana sp. n., T. orc sp. n., T. robitika sp. n.,T. sargina sp. n., T. yammer sp. n., and T. vohitra sp. n. A lectotype and several paralectotypes of T. steinheili are desig-nated. Tetramorium marginatum is the central species of the T. marginatum group, which also includes the five newly de-scribed species T. valky sp. n., T. hector sp. n., T. norvigi sp. n., T. shamshir sp. n., and T. silvicola sp. n. The T. bonibonyand T. tsingy groups represent completely new groups that consist entirely of previously unknown, undescribed species.The first group holds the new species T. bonibony sp. n., T. kali sp. n., T. sada sp. n., T. nosybe sp. n., T. olana sp. n., T.popell sp. n., and T. trafo sp. n. and T. vony sp. n. The last group, the T. tsingy group, only contains the two species T. tyrionsp. n. and T. tsingy sp. n., both among the rarest Tetramorium species in Madagascar. All groups are fully revised withillustrated species-level identification keys, and all species are described/re-described and illustrated with high qualitymontage images. In addition, the current status of the Malagasy Tetramorium species groups is discussed and further modifications are proposed.

RNA silencing as a tool for exploring gene function in ascomycete fungi

2005 ◽  
Vol 42 (4) ◽  
pp. 275-283 ◽  
Author(s):  
Hitoshi Nakayashiki ◽  
Shugo Hanada ◽  
Nguyen Bao Quoc ◽  
Naoki Kadotani ◽  
Yukio Tosa ◽  
...  
Keyword(s):  
Gene Function ◽  
Rna Silencing ◽  
Ascomycete Fungi

scholarly journals A comparative study of metagenomics analysis pipelines at the species level

2016 ◽  
Author(s):  
Yee Voan Teo ◽  
Nicola Neretti
Keyword(s):  
Comparative Study ◽  
Species Level ◽  
Marker Genes ◽  
Closely Related Species ◽  
Full Reference ◽  
Quantification Accuracy ◽  
Reference Genomes ◽  
Metagenomics Analysis ◽  
Higher Sensitivity

AbstractMany metagenomics classification tools have been developed with the rapid growth of the metagenomics field. However, the classification of closely related species remains a challenge for this field. Here, we compared MetaPhlAn2, kallisto and Kraken for their performances in two metagenomics settings, human metagenomics and environmental metagenomics. Our comparative study showed that kallisto demonstrated higher sensitivity than MetaPhlAn2 and Kraken and better quantification accuracy than Kraken at the species level. We also showed that classification tools that run on full reference genomes misidentified many species that were not truly present. In order to reduce false positives, we introduced marker genes from MetaPhlAn2 into our pipeline, which uses kallisto for the classification step, as an additional filtering step for species detection.

scholarly journals Mechanisms of Manganese(II) Oxidation by Filamentous Ascomycete Fungi Vary With Species and Time as a Function of Secretome Composition

2021 ◽  
Vol 12 ◽  
Author(s):  
Carolyn A. Zeiner ◽  
Samuel O. Purvine ◽  
Erika Zink ◽  
Si Wu ◽  
Ljiljana Paša-Tolić ◽  
...  
Keyword(s):  
Physiological Role ◽  
Oxidative Capacity ◽  
White Rot ◽  
Lignocellulose Degradation ◽  
Filamentous Ascomycete ◽  
Solid Substrates ◽  
Gmc Oxidoreductase ◽  
Ascomycete Fungi ◽  
Species Specific ◽  
Glyoxal Oxidase

Manganese (Mn) oxides are among the strongest oxidants and sorbents in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and manganese peroxidases in association with lignocellulose degradation, the mechanisms by which filamentous Ascomycete fungi oxidize Mn(II) and a physiological role for Mn(II) oxidation in these organisms remain poorly understood. Here we use a combination of chemical and in-gel assays and bulk mass spectrometry to demonstrate secretome-based Mn(II) oxidation in three phylogenetically diverse Ascomycetes that is mechanistically distinct from hyphal-associated Mn(II) oxidation on solid substrates. We show that Mn(II) oxidative capacity of these fungi is dictated by species-specific secreted enzymes and varies with secretome age, and we reveal the presence of both Cu-based and FAD-based Mn(II) oxidation mechanisms in all 3 species, demonstrating mechanistic redundancy. Specifically, we identify candidate Mn(II)-oxidizing enzymes as tyrosinase and glyoxal oxidase in Stagonospora sp. SRC1lsM3a, bilirubin oxidase in Stagonospora sp. and Paraconiothyrium sporulosum AP3s5-JAC2a, and GMC oxidoreductase in all 3 species, including Pyrenochaeta sp. DS3sAY3a. The diversity of the candidate Mn(II)-oxidizing enzymes identified in this study suggests that the ability of fungal secretomes to oxidize Mn(II) may be more widespread than previously thought.

scholarly journals Adding context to the pneumococcal core genes – a bioinformatic analysis of the intergenic pangenome of Streptococcus pneumoniae

2021 ◽  
Author(s):  
Flemming Damgaard Nielsen ◽  
Jakob Møller-Jensen ◽  
Mikkel Girke Jørgensen
Keyword(s):  
Streptococcus Pneumoniae ◽  
Core Genome ◽  
Biological Function ◽  
Bioinformatic Analysis ◽  
Bacterial Pathogenicity ◽  
The Core ◽  
Intergenic Regions ◽  
Crucial Information ◽  
Genetic Context ◽  
Core Genes

AbstractWhole genome sequencing offers great opportunities for linking genotypes to phenotypes aiding in our understanding of human disease and bacterial pathogenicity. However, these analyses often overlook non-coding intergenic regions (IGRs). By disregarding the IGRs, crucial information is lost, as genes have little biological function without expression. In this study, we present the first complete pangenome of the important human pathogen Streptococcus pneumoniae (pneumococcus), spanning both the genes and IGRs. We show that the pneumococcus species retains a small core genome of IGRs that are present across all isolates. Gene expression is highly dependent on these core IGRs, and often several copies of these core IGRs are found across each genome. Core genes and core IGRs show a clear linkage as 81% of core genes are associated with core IGRs. Additionally, we identify a single IGR within the core genome that is always occupied by one of two highly distinct sequences, scattered across the phylogenetic tree. Their distribution indicates that this IGR is transferred between isolates through horizontal regulatory transfer independent of the flanking genes and that each type likely serves different regulatory roles depending on their genetic context.

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