Review
Infectious Diseases
Shian Lai, Quan Zhang, Lin Jin
Summary: Due to the abuse of antibiotics, an increasing number of drug-resistant bacterial strains have emerged, posing a serious threat to human and animal health. Antimicrobial peptides (AMPs) have proven to be one of the most effective solutions, as they exhibit low propensity for drug resistance and possess remarkable antimicrobial effects. Among them, cyclic AMPs, especially macrocyclic ones, have garnered extensive attention.
Article
Biochemistry & Molecular Biology
Hideaki Oikawa, Yusuke Mizunoue, Takemichi Nakamura, Eri Fukushi, Jiang Yulu, Taro Ozaki, Atsushi Minami
Summary: This study elucidates the structure and biosynthetic pathway of Albopeptins produced by Streptomyces albofaciens JC-82-120 using degradation, chemical synthesis, NMR data analysis, and bioinformatics analysis.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Jan Viglas, Simona Dobiasova, Jitka Viktorova, Tomas Ruml, Vanda Repiska, Petra Olejnikova, Helena Gbelcova
Summary: This study investigated the production of peptaibols by Trichoderma atroviride O1 and their antibacterial and anticancer activity against drug-sensitive and multi-drug resistant bacteria and cancer cell lines. The results showed that peptaibols exhibited significant inhibitory effects on the growth of methicillin-resistant Staphylococcus aureus and human breast cancer and ovarian cancer cell lines.
Letter
Biochemistry & Molecular Biology
Daniel L. Machell, Mathias H. Hansen, Max J. Cryle
Summary: Detection of pyrophosphate is crucial for quantifying enzyme activity, especially adenylation domain activity in non-ribosomal peptide synthesis. After screening, viable replacement enzymes with higher activity have been identified, allowing the continued use of the established online assay for pyrophosphate detection.
Article
Plant Sciences
Xiao Lin, Zhenzhou Tang, Yuman Gan, Zhengyuan Li, Xiaowei Luo, Chenghai Gao, Longyan Zhao, Ling Chai, Yonghong Liu
Summary: Seven new 18-residue peptaibols, named trichorzins A-G (1-7), were isolated from the sponge-derived fungus Trichoderma sp. GXIMD 01001. Their structures and configurations were characterized using various analytical techniques. The compounds showed significant cytotoxicity against human carcinoma cell lines, but did not exhibit potent antibacterial activity.
JOURNAL OF NATURAL PRODUCTS
(2023)
Review
Biotechnology & Applied Microbiology
Leandro Pereira-Dias, Paulo R. Oliveira-Pinto, Juliana O. Fernandes, Laura Regalado, Rafael Mendes, Catia Teixeira, Nuno Mariz-Ponte, Paula Gomes, Conceicao Santos
Summary: Agricultural systems require low-cost, safe antibiotics to protect crops from pests and diseases. Peptaibiotics have shown potential as alternatives to agrochemicals, with antibacterial, antifungal, and antiviral activity, and the ability to induce plant resistance against phytopathogens. However, their low solubility and difficulty in synthesis and purification have limited their application in agriculture. This review provides a comprehensive analysis of peptaibiotics, including their classification, biosynthesis, relevance to plant protection, and mode of action against phytopathogens, as well as strategies to enhance their solubility and production.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Biochemistry & Molecular Biology
Aaron P. Decker, Abraham F. Mechesso, Guangshun Wang
Summary: Unlike the alpha-helical and beta-sheet antimicrobial peptides (AMPs), amino acid-rich AMPs have limited knowledge. This article conducted a systematic study on rich AMPs (>25%) from different life kingdoms using the Antimicrobial Peptide Database (APD) and program R. Of the 3425 peptides analyzed, 724 rich AMPs were identified. The distribution of rich AMPs differs among animals, bacteria, and plants. Certain amino acids are frequently observed in rich AMPs, while others are occasionally observed or not yet found. These findings can guide peptide design and rich AMPs show promise as future antibiotics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Husen M. Umer, Enrique Audain, Yafeng Zhu, Julianus Pfeuffer, Timo Sachsenberg, Janne Lehtio, Rui Branca, Yasset Perez-Riverol
Summary: The pypgatk package and pgdb workflow have been implemented to create proteogenomics databases based on ENSEMBL resources. The tools can generate protein sequences from different types of transcripts and take into account the impact of genomic variants on protein sequences. Using these tools, researchers have reanalyzed public datasets and identified a significant number of novel protein sequences.
Article
Plant Sciences
Annika Jagels, Donovon A. Adpressa, Elizabeth N. Kaweesa, Mark McCauley, Benjamin Philmus, James A. Strother, Sandra Loesgen
Summary: This study reports a chemically underexplored fungus Myrotheciuminundatum with a high number of putative biosynthetic gene clusters. New linear lipopeptides were discovered through non-genetic gene activation experiments. These lipopeptides exhibit broad-spectrum toxicity against cancer cell lines, pathogenic bacteria, and fungi, indicating their potential as important antitumor and antimicrobial agents.
JOURNAL OF NATURAL PRODUCTS
(2023)
Review
Biotechnology & Applied Microbiology
I. A. Gavryushina, M. L. Georgieva, A. E. Kuvarina, V. S. Sadykova
Summary: Today's shortage of effective antimicrobial agents can be addressed by utilizing antimicrobial peptides, which are naturally produced compounds with various biological activities like antibacterial, antifungal, and anticancer properties. This review focuses on the sources, direct surface applications, and mode of action of peptaibols produced by filamentous fungi, known for their anticancer and antifungal activities.
APPLIED BIOCHEMISTRY AND MICROBIOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Li Tian, Shi Shi, Xiangmei Zhang, Fubo Han, Huijun Dong
Summary: Glycopeptide antibiotics (GPAs) are considered as the last resort for treating severe infections caused by multidrug-resistant Gram-positive pathogens. However, the increasing prevalence of Gram-positive resistant strain superbugs has posed a challenge, requiring further study and modification of GPAs.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Maria Giovanna Lizio, Mario Campana, Matteo De Poli, Damien F. Jefferies, William Cullen, Valery Andrushchenko, Nikola P. Chmel, Petr Bour, Syma Khalid, Jonathan Clayden, Ewan Blanch, Alison Rodger, Simon J. Webb
Summary: This study used various spectroscopic techniques to investigate the mechanism of action of peptides rich in Aib segments in cell membranes. The peptides were found to quickly orient in the membranes, with evidence of chiral interactions. Chiro-optical spectroscopies can help reveal the mechanism of action of antimicrobial peptides.
Article
Biochemistry & Molecular Biology
Sergey V. Kravchenko, Pavel A. Domnin, Sergei Y. Grishin, Nikita A. Vershinin, Elena V. Gurina, Anastasiia A. Zakharova, Viacheslav N. Azev, Leila G. Mustaeva, Elena Y. Gorbunova, Margarita I. Kobyakova, Alexey K. Surin, Roman S. Fadeev, Olga S. Ostroumova, Svetlana A. Ermolaeva, Oxana V. Galzitskaya
Summary: Combining antimicrobial peptides with cell-penetrating peptides has potential in enhancing antimicrobial activity against various bacterial strains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Sergei Y. Grishin, Pavel A. Domnin, Sergey Kravchenko, Viacheslav N. Azev, Leila G. Mustaeva, Elena Y. Gorbunova, Margarita Kobyakova, Alexey K. Surin, Maria A. Makarova, Stanislav R. Kurpe, Roman S. Fadeev, Alexey S. Vasilchenko, Victoria V. Firstova, Svetlana A. Ermolaeva, Oxana Galzitskaya
Summary: The development and testing of new antimicrobial peptides, including a unique hybrid peptide combining membrane penetrating peptide and amyloidogenic peptide segments, showed promise in inhibiting the growth of pathogens such as Pseudomonas aeruginosa. The study demonstrated antibacterial activity comparable to gentamicin sulfate, with no toxicity to eukaryotic cells, indicating the potential for new antimicrobial drug development against P. aeruginosa using these hybrid peptides.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemical Research Methods
Maryam Mahjoubin-Tehran, Samaneh Rezaei, Amin Jalili, Amirhossein Sahebkar, Seyed Hamid Aghaee-Bakhtiari
Summary: MicroRNAs play a crucial role in regulating gene expression and signaling pathways, making them important regulators in cellular processes and diseases. Understanding the relationship between miRNAs and diseases is of great interest in research, and databases offer valuable information for identifying critical miRNAs and their clinical applications. This review summarizes miRNAs-disease databases and their limitations, providing researchers with a comprehensive reference and developers/designers with a guideline for database features and limitations.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Verena Speckbacher, Susanne Zeilinger, Stefan Zimmermann, Christopher A. Mayhew, Helmut Wiesenhofer, Veronika Ruzsanyi
Summary: The study established a method for on-line analysis of microbial volatile organic compounds (MVOCs) during cultivation of different fungi using GC-IMS, revealing the time- and light-dependent release of MVOCs by F. oxysporum and T. atroviride. Various volatile compounds were detected, with alcohols being the majority, along with ketones, esters, and aldehydes, showing characteristic profiles during cultivation depending on axenic or co-cultivation, exposure to light, and fungal species.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Microbiology
Lea Atanasova, Dubraska Moreno-Ruiz, Clemens Grunwald-Gruber, Viktoria Hell, Susanne Zeilinger
Summary: This study characterized the transmembrane protein Dfg5 in the fungal mycoparasite Trichoderma atroviride, showing its crucial role in hyphal morphology, cell wall remodeling, protein release, and gene expression. Dfg5 was found to control physiological properties such as osmotic stress resistance, hyphal morphology, and cell wall stability in T. atroviride.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Julia Embacher, Sigrid Neuhauser, Susanne Zeilinger, Martin Kirchmair
Summary: The dry rot fungus Serpula lacrymans causes severe structural damage to construction timber, necessitating costly restoration procedures. Research has shown that S. lacrymans harbors various co-existing bacteria, with differences in communities associated with different fungal parts. Some bacteria in co-culture can impact the growth and pigment production of S. lacrymans.
Article
Microbiology
Dubraska Moreno-Ruiz, Linda Salzmann, Mark D. Fricker, Susanne Zeilinger, Alexander Lichius
Summary: Trichoderma atroviride acts as a biological control agent against fungal plant pathogens, and the perception of prey-derived signals and regulation of morphogenetic responses are crucial for successful mycoparasitism. The fungus experiences significant polarity stress when approaching its fungal preys, with responses varying depending on the prey species and interaction stage, reflecting the high selectivity of the signalling process. Deletion of MAP kinases Tmk1 and Tmk3 affects tip polarization, chemotropic growth, and contact-induced morphogenesis, underscoring the importance of a sensitive polarized tip growth apparatus for successful mycoparasitism.
Article
Chemistry, Analytical
Bernhard Seidl, Rainer Schuhmacher, Christoph Bueschl
Summary: The use of stable isotopically labeled tracers is an effective method in detecting and tracking metabolites. However, there is currently no software tool available for automatically searching user-defined isotopolog patterns in LC-HRMS data. CPExtract is a versatile software tool that allows high-throughput search for isotopolog patterns in LC-HRMS data.
ANALYTICAL CHEMISTRY
(2022)
Article
Microbiology
Jia Gao, Max Wenderoth, Maria Doppler, Rainer Schuhmacher, Doris Marko, Reinhard Fischer
Summary: The study found that the growth and toxin production of the filamentous fungus Alternaria alternata are actually regulated by the same set of enzymes, especially those closely related to melanin biosynthesis pathway. This discovery may alter the previous understanding of the range of fungi producing certain specific toxins.
Review
Mycology
Prasun K. Mukherjee, Artemio Mendoza-Mendoza, Susanne Zeilinger, Benjamin A. Horwitz
Summary: Trichoderma spp. are widely used as plant disease biocontrol agents in agriculture, mainly through mycoparasitism to reduce pathogen inocula. They exhibit different nutritional modes and cause varying levels of damage to host cells in their interactions.
FUNGAL BIOLOGY REVIEWS
(2022)
Article
Biochemical Research Methods
Maria Doppler, Christoph Bueschl, Florian Ertl, Jakob Woischitzschlaeger, Alexandra Parich, Rainer Schuhmacher
Summary: Phenylalanine is an important precursor for many secondary plant metabolites. Recent studies have shown that defense metabolites derived from phenylalanine are induced in wheat with fungal disease, and some of them are incorporated into the cell wall. A new approach was developed to screen phenylalanine-derived metabolites. The study also demonstrated the suitability of this method for typical metabolomics applications.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Daniel Flatschacher, Verena Speckbacher, Susanne Zeilinger
Summary: qRAT is a stand-alone desktop application based on R that automatically processes raw output data from any qPCR machine, offering a comprehensive, user-friendly solution for RT-qPCR data analysis.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Anna K. Atanasoff-Kardjalieff, Bernhard Seidl, Katharina Steinert, Constantin G. Daniliuc, Rainer Schuhmacher, Hans-Ulrich Humpf, Svetlana Kalinina, Lena Studt-Reinhold
Summary: Fusarium mangiferae causes the economically significant mango malformation disease (MMD) on young mango trees and seedlings, leading to crop losses. Additionally, it produces secondary metabolites (SMs) that may contaminate the harvest. This study identifies the impact of the H3 K9-specific histone methyltransferase FmKmt1 on the expression of FmPKS8, a previously unknown polyketide synthase. The biosynthetic gene cluster (BGC) of FmPKS8 is determined, and its activity is linked to the production of fusamarins.
Article
Ecology
Julia Embacher, Manuela Seehauser, Christoph Kappacher, Stefan Stuppner, Susanne Zeilinger, Martin Kirchmair, Sigrid Neuhauser
Summary: Serpula lacrymans causes damage in timber by decomposing cellulose and hemicellulose. It interacts with bacteria and fungi, resulting in stress and changed behavior of the partners. Stress induces the production of bioactive metabolites and pigments, which exhibit unspecific patterns and can be induced even without direct contact with other microbes.
Article
Biochemistry & Molecular Biology
Christina Maisl, Maria Doppler, Bernhard Seidl, Christoph Bueschl, Rainer Schuhmacher
Summary: Lyophilization is commonly used to stabilize biological samples or concentrate extracts. However, it may alter the metabolic composition or cause the loss of metabolites. This study investigated the performance of lyophilization in wheat root samples and found that it altered the metabolic composition and led to the loss or change of metabolite abundances.
Review
Mycology
Julia Embacher, Susanne Zeilinger, Martin Kirchmair, Luis M. Rodriguez-r, Sigrid Neuhauser
Summary: Microbial biodeterioration of timber and woody material in buildings can lead to costly restoration procedures, with the fungus Serpula lacrymans causing the most severe damages in Europe. Research on microorganisms inhabiting the same habitat and interacting with the dry-rot fungus is not comprehensive. Bacterial-fungal interactions in dead wood have significant impacts on the partners involved, ranging from antagonistic to beneficial.
FUNGAL BIOLOGY REVIEWS
(2023)
Article
Microbiology
Kristina Missbach, Daniel Flatschacher, Christoph Bueschl, Jonathan Matthew Samson, Stefan Leibetseder, Martina Marchetti-Deschmann, Susanne Zeilinger, Rainer Schuhmacher
Summary: Many studies have neglected the influence of light on fungal secondary metabolite production. In this study, the effect of different light regimes on Trichoderma atroviride secondary metabolite production was systematically determined using metabolomics analysis. It was found that reduced light conditions maximize secondary metabolite production.
