scholarly journals Phylogenetic Assignment of the Fungicolous Hypoxylon invadens (Ascomycota, Xylariales) and Investigation of its Secondary Metabolites

2020 ◽  
Vol 8 (9) ◽  
pp. 1397 ◽  
Author(s):  
Kevin Becker ◽  
Christopher Lambert ◽  
Jörg Wieschhaus ◽  
Marc Stadler
Keyword(s):  
Secondary Metabolites ◽  
Rna Polymerase Ii ◽  
High Resolution Mass Spectrometry ◽  
Large Subunit ◽  
Submerged Cultivation ◽  
Preparative Chromatography ◽  
Sequence Information ◽  
Internal Transcribed Spacer Region ◽  
Multiple Sequence ◽  
And Function

The ascomycete Hypoxylon invadens was described in 2014 as a fungicolous species growing on a member of its own genus, H.fragiforme, which is considered a rare lifestyle in the Hypoxylaceae. This renders H.invadens an interesting target in our efforts to find new bioactive secondary metabolites from members of the Xylariales. So far, only volatile organic compounds have been reported from H.invadens, but no investigation of non-volatile compounds had been conducted. Furthermore, a phylogenetic assignment following recent trends in fungal taxonomy via a multiple sequence alignment seemed practical. A culture of H.invadens was thus subjected to submerged cultivation to investigate the produced secondary metabolites, followed by isolation via preparative chromatography and subsequent structure elucidation by means of nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry (HR-MS). This approach led to the identification of the known flaviolin (1) and 3,3-biflaviolin (2) as the main components, which had never been reported from the order Xylariales before. Assessment of their antimicrobial and cytotoxic effects via a panel of commonly used microorganisms and cell lines in our laboratory did not yield any effects of relevance. Concurrently, genomic DNA from the fungus was used to construct a multigene phylogeny using ribosomal sequence information from the internal transcribed spacer region (ITS), the 28S large subunit of ribosomal DNA (LSU), and proteinogenic nucleotide sequences from the second largest subunit of the DNA-directed RNA polymerase II (RPB2) and β-tubulin (TUB2) genes. A placement in a newly formed clade with H.trugodes was strongly supported in a maximum-likelihood (ML) phylogeny using sequences derived from well characterized strains, but the exact position of said clade remains unclear. Both, the chemical and the phylogenetic results suggest further inquiries into the lifestyle of this unique fungus to get a better understanding of both, its ecological role and function of its produced secondary metabolites hitherto unique to the Xylariales.

Inocybe griseorubida, a new species of Pseudosperma clade from tropical India

Phytotaxa ◽  
2015 ◽  
Vol 221 (2) ◽  
pp. 166 ◽  
Author(s):  
K. P. Deepna Latha ◽  
Patinjareveettil Manimohan
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Rna Polymerase Ii ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Similar Species ◽  
Internal Transcribed Spacer Region ◽  
Comprehensive Description ◽  
Kerala State ◽  
A New Species

Inocybe griseorubida sp. nov. is described from Kerala State, India. A comprehensive description, photographs, and comparisons with phenetically similar species are provided. The nuclear ribosomal internal transcribed spacer region (ITS), a portion of the nuclear ribosomal large subunit (nLSU) and a portion of the nuclear second-largest subunit of RNA polymerase II (rpb2) gene of this species were sequenced and analyzed. Phylogenetic analysis of rpb2 sequences confirmed both the novelty of the species and its placement within the Pseudosperma clade.

scholarly journals Unveiling the Hidden Diversity of Rock-Inhabiting Fungi: Chaetothyriales from China

2020 ◽  
Vol 6 (4) ◽  
pp. 187
Author(s):  
Wei Sun ◽  
Lei Su ◽  
Shun Yang ◽  
Jingzu Sun ◽  
Bingjie Liu ◽  
...  
Keyword(s):  
New Species ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Small Subunit ◽  
Internal Transcribed Spacer Region ◽  
Natural Rock ◽  
Rock Inhabiting Fungi

Rock-inhabiting fungi (RIF) are nonlichenized fungi that naturally colonize rock surfaces and subsurfaces. The extremely slow growth rate and lack of distinguishing morphological characteristics of RIF resulted in a poor understanding on their biodiversity. In this study, we surveyed RIF colonizing historical stone monuments and natural rock formations from throughout China. Among over 1000 isolates, after preliminary delimitation using the internal transcribed spacer region (ITS) sequences, representative isolates belonging to Trichomeriaceae and Herpotrichiellaceae were selected for a combined analysis of ITS and the nuclear ribosomal large subunit (nucLSU) to determine the generic placements. Eight clades representing seven known genera and one new genus herein named as Anthracina were placed in Trichomeriaceae. While, for Herpotrichiellaceae, two clades corresponded to two genera: Cladophialophora and Exophiala. Fine-scale phylogenetic analyses using combined sequences of the partial actin gene (ACT), ITS, mitochondrial small subunit ribosomal DNA (mtSSU), nucLSU, the largest subunit of RNA polymerase II (RPB1), small subunit of nuclear ribosomal RNA gene (SSU), translation elongation factor (TEF), and β-tubulin gene (TUB) revealed that these strains represented 11 and 6 new species, respectively, in Trichomeriaceae and Herpotrichiellaceae. The 17 new species were described, illustrated for their morphologies and compared with similar taxa. Our study demonstrated that the diversity of RIF is surprisingly high and still poorly understood. In addition, a rapid strategy for classifying RIF was proposed to determine the generic and familial placements through preliminary ITS and nucLSU analyses, followed by combined analyses of five loci selected from ACT, ITS, mtSSU, nucLSU, RPB1, and/or the second subunit of RNA polymerase II gene (RPB2), SSU, TEF, and TUB regions to classify RIF to the species level.

New and noteworthy species of white Entoloma (Agaricales, Entolomataceae) in China

Phytotaxa ◽  
2015 ◽  
Vol 205 (2) ◽  
pp. 99 ◽  
Author(s):  
Xiao-Lan He ◽  
Tai-Hui Li ◽  
Wei-Hong Peng ◽  
Bing-Cheng Gan
Keyword(s):  
Phylogenetic Analysis ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Monophyletic Group ◽  
Southwestern China ◽  
High Altitudes ◽  
Internal Transcribed Spacer Region ◽  
The Common

Three species of Entoloma with white basidioma in subgenus Alboleptonia from China are reported in this paper. Entoloma crocotillum is described as new to science from high altitudes in southwestern China. It is characterized by the small, white to pinkish pileus covered with matted-appressed fibrils, relatively large basidiospores with 5–6 angles, and the common presence of clamp-connections. Entoloma sulcatum, a new Chinese record, and E. stylophorum are documented based on new collections. Additionally, ITS (internal transcribed spacer region), nLSU (nuclear large subunit), and RPB2 (RNA polymerase II second largest subunit) sequences of E. crocotillum were successfully generated, and the phylogenetic positions of the three species among Alboleptonia species and other entolomatoid groups are preliminarily analyzed based on the combined nLSU and RPB2 dataset. The phylogenetic analysis showed that E. crocotillum is most closely related to E. sericellum and that Alboleptonia is not a monophyletic group.

A new species of Inocybe representing the Nothocybe lineage

Phytotaxa ◽  
2016 ◽  
Vol 267 (1) ◽  
pp. 40 ◽  
Author(s):  
K. P. DEEPNA LATHA ◽  
PATINJAREVEETTIL MANIMOHAN ◽  
P. BRANDON MATHENY
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Rna Polymerase Ii ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Internal Transcribed Spacer Region ◽  
Comprehensive Description ◽  
Line Drawings ◽  
Kerala State ◽  
A New Species

Inocybe distincta sp. nov. is described from Kerala State, India. A comprehensive description, photographs, line drawings and comments are provided. The nuclear ribosomal internal transcribed spacer region (ITS), a portion of the nuclear ribosomal large subunit (nrLSU) and a portion of the nuclear second-largest subunit of RNA polymerase II (RPB2) gene of this species were sequenced and analyzed. BLASTn searches using nrLSU and RPB2 sequences and subsequent ML phylogenetic analysis of combined nrLSU and RPB2 sequences confirmed that Inocybe distincta is a representative of the Nothocybe lineage. As the Nothocybe lineage is assumed to have affinities to I. cutifracta, and as there are different interpretations of that species, we examined the holotype of I. cutifracta collected by T. Petch and another collection from Sri Lanka identified as I. cutifracta by D. N. Pegler, and we present here our observations on these collections.

scholarly journals Morinagadepsin, a Depsipeptide from the Fungus Morinagamyces vermicularis gen. et comb. nov.

2021 ◽  
Vol 9 (6) ◽  
pp. 1191
Author(s):  
Karen Harms ◽  
Frank Surup ◽  
Marc Stadler ◽  
Alberto Miguel Stchigel ◽  
Yasmina Marin-Felix
Keyword(s):  
Antimicrobial Activity ◽  
High Resolution Mass Spectrometry ◽  
Large Subunit ◽  
Building Blocks ◽  
2D Nmr ◽  
Partial Hydrolysis ◽  
Phylogenetic Study ◽  
Internal Transcribed Spacer Region ◽  
Mammalian Cell Lines ◽  
Hydrolysis Of

The new genus Morinagamyces is introduced herein to accommodate the fungus Apiosordaria vermicularis as inferred from a phylogenetic study based on sequences of the internal transcribed spacer region (ITS), the nuclear rDNA large subunit (LSU), and partial fragments of ribosomal polymerase II subunit 2 (rpb2) and β-tubulin (tub2) genes. Morinagamyces vermicularis was analyzed for the production of secondary metabolites, resulting in the isolation of a new depsipeptide named morinagadepsin (1), and the already known chaetone B (3). While the planar structure of 1 was elucidated by extensive 1D- and 2D-NMR analysis and high-resolution mass spectrometry, the absolute configuration of the building blocks Ala, Val, and Leu was determined as -l by Marfey’s method. The configuration of the 3-hydroxy-2-methyldecanyl unit was assigned as 22R,23R by J-based configuration analysis and Mosher’s method after partial hydrolysis of the morinagadepsin to the linear derivative compound 2. Compound 1 showed cytotoxic activity against the mammalian cell lines KB3.1 and L929, but no antimicrobial activity against the fungi and bacteria tested was observed, while 2 was inactive. Compound 3 was weakly cytotoxic against the cell line L929, but did not show any antimicrobial activity.

ConDo: protein domain boundary prediction using coevolutionary information

2018 ◽  
Vol 35 (14) ◽  
pp. 2411-2417 ◽  
Author(s):  
Seung Hwan Hong ◽  
Keehyoung Joo ◽  
Jooyoung Lee
Keyword(s):  
Long Range ◽  
Domain Boundary ◽  
Prediction Method ◽  
Protein Domain ◽  
Supplementary Information ◽  
Sequence Information ◽  
Multiple Sequence ◽  
Domain Boundary Prediction ◽  
Correlation Information ◽  
And Function

AbstractMotivationDomain boundary prediction is one of the most important problems in the study of protein structure and function. Many sequence-based domain boundary prediction methods are either template-based or machine learning (ML) based. ML-based methods often perform poorly due to their use of only local (i.e. short-range) features. These conventional features such as sequence profiles, secondary structures and solvent accessibilities are typically restricted to be within 20 residues of the domain boundary candidate.ResultsTo address the performance of ML-based methods, we developed a new protein domain boundary prediction method (ConDo) that utilizes novel long-range features such as coevolutionary information in addition to the aforementioned local window features as inputs for ML. Toward this purpose, two types of coevolutionary information were extracted from multiple sequence alignment using direct coupling analysis: (i) partially aligned sequences, and (ii) correlated mutation information. Both the partially aligned sequence information and the modularity of residue–residue couplings possess long-range correlation information.Availability and implementationhttps://github.com/gicsaw/ConDo.gitSupplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals New endemic Fusarium species hitch-hiking with pathogenic Fusarium strains causing Panama disease in small-holder banana plots in Indonesia

2019 ◽  
Vol 43 (1) ◽  
pp. 48-69 ◽  
Author(s):  
N. Maryani ◽  
M. Sandoval-Denis ◽  
L. Lombard ◽  
P.W. Crous ◽  
G.H.J. Kema
Keyword(s):  
Rna Polymerase Ii ◽  
Fusarium Wilt ◽  
Species Complex ◽  
Plant Pathogens ◽  
Fusarium Species ◽  
Large Subunit ◽  
Fusarium Fujikuroi ◽  
Internal Transcribed Spacer Region ◽  
Species Complexes ◽  
Fusarium Wilt Of Banana

Fusarium species are well known for their abundance, diversity and cosmopolitan life style. Many members of the genus Fusarium are associated with plant hosts, either as plant pathogens, secondary invaders, saprotrophs, and/or endophytes. We previously studied the diversity of Fusarium species in the Fusarium oxysporum species complex (FOSC) associated with Fusarium wilt of banana in Indonesia. In that study, several Fusarium species not belonging to the FOSC were found to be associated with Fusarium wilt of banana. These Fusarium isolates belonged to three Fusarium species complexes, which included the Fusarium fujikuroi species complex (FFSC), Fusarium incarnatum-equiseti species complex (FIESC) and the Fusarium sambucinum species complex (FSSC). Using a multi-gene phylogeny that included partial fragments of the beta-tubulin (tub), calmodulin (cmdA), translation elongation factor 1-alpha (tef1), the internal transcribed spacer region of the rDNA (ITS), the large subunit of the rDNA (LSU), plus the RNA polymerase II large subunit (rpb1) and second largest subunit (rpb2) genes, we were able to identify and characterise several of these as new Fusarium species in the respective species complexes identified in this study.

Inocybe gregaria, a new species of the Inosperma clade from tropical India

Phytotaxa ◽  
2016 ◽  
Vol 286 (2) ◽  
pp. 107 ◽  
Author(s):  
K. P. DEEPNA LATHA ◽  
PATINJAREVEETTIL MANIMOHAN
Keyword(s):  
New Species ◽  
Rna Polymerase Ii ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Molecular Data ◽  
Internal Transcribed Spacer Region ◽  
Comprehensive Description ◽  
Morphological And Molecular Data ◽  
Kerala State ◽  
A New Species

Inocybe gregaria sp. nov. is described from Kerala State, India, based on morphological and molecular data. A comprehensive description, photographs, and comparisons with phenetically similar and phylogenetically related species are provided. The nuclear ribosomal internal transcribed spacer region (nrITS), a portion of the nuclear ribosomal large subunit (nrLSU) and a portion of the nuclear second-largest subunit of RNA polymerase II (rpb2) gene of this species were sequenced and analyzed. BLASTn searches using LSU and rpb2 sequences and subsequent ML phylogram of combined LSU and rpb2 sequences revealed that I. gregaria is conspecific with Inocybe sp. ZT8944, a collection assigned to the Inosperma clade that remains undescribed.

Depletion and Reconstitution of Active E. Coli Ribosomes

1975 ◽  
Vol 33 ◽  
pp. 640-641
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Protein Biosynthesis ◽  
Large Subunit ◽  
High Resolution Electron Microscopy ◽  
Small Subunit ◽  
Structure And Function ◽  
Biologically Active ◽  
Biological Macromolecules ◽  
E Coli ◽  
Resolution Electron ◽  
And Function

Correlations between structure and function of biological macromolecules have been studied intensively for many years, mostly by indirect methods. High resolution electron microscopy is a unique tool which can provide such information directly by comparing the conformation of biopolymers in their biologically active and inactive state. We have correlated the structure and function of ribosomes, ribonucleoprotein particles which are the site of protein biosynthesis. 70S E. coli ribosomes, used in this experiment, are composed of two subunits - large (50S) and small (30S). The large subunit consists of 34 proteins and two different ribonucleic acid molecules. The small subunit contains 21 proteins and one RNA molecule. All proteins (with the exception of L7 and L12) are present in one copy per ribosome.This study deals with the changes in the fine structure of E. coli ribosomes depleted of proteins L7 and L12. These proteins are unique in many aspects.

A Mucin-Specific Protease Enables Molecular and Functional Analysis of Human Cancer-Associated Mucins

2018 ◽  
Author(s):  
Stacy A. Malaker ◽  
Kayvon Pedram ◽  
Michael J. Ferracane ◽  
Elliot C. Woods ◽  
Jessica Kramer ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Mechanisms ◽  
Cultured Cells ◽  
High Resolution Mass Spectrometry ◽  
Human Cancer ◽  
Glycosylation Sites ◽  
Bacterial Protease ◽  
Specific Protease ◽  
To Come ◽  
And Function

<div> <div> <div> <p>Mucins are a class of highly O-glycosylated proteins that are ubiquitously expressed on cellular surfaces and are important for human health, especially in the context of carcinomas. However, the molecular mechanisms by which aberrant mucin structures lead to tumor progression and immune evasion have been slow to come to light, in part because methods for selective mucin degradation are lacking. Here we employ high resolution mass spectrometry, polymer synthesis, and computational peptide docking to demonstrate that a bacterial protease, called StcE, cleaves mucin domains by recognizing a discrete peptide-, glycan-, and secondary structure- based motif. We exploited StcE’s unique properties to map glycosylation sites and structures of purified and recombinant human mucins by mass spectrometry. As well, we found that StcE will digest cancer-associated mucins from cultured cells and from ovarian cancer patient-derived ascites fluid. Finally, using StcE we discovered that Siglec-7, a glyco-immune checkpoint receptor, specifically binds sialomucins as biological ligands, whereas the related Siglec-9 receptor does not. Mucin-specific proteolysis, as exemplified by StcE, is therefore a powerful tool for the study of glycoprotein structure and function and for deorphanizing mucin-binding receptors. </p> </div> </div> </div>

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