Article
Microbiology
Tobias Busche, Hana Dostalova, Lenka Rucka, Jiri Holatko, Ivan Barvik, Vaclav Stepanek, Miroslav Patek, Joern Kalinowski
Summary: The sigma H and sigma E subunits of Corynebacterium glutamicum RNA polymerase belong to Group 4 of sigma factors, also called extracytoplasmic function (ECF) sigma factors. While the genes of the C. glutamicum sigma(Eta) regulon involved in heat and oxidative stress response have been studied, the genes of the sigma(E) regulon, involved in cell surface stress response, have not been explored until now. Differential gene expression analysis revealed a significant overlap between the sigma(Eta) and sigma(E) regulons, and identified genes involved in protein quality control, regulation of Clp proteases, and membrane integrity maintenance.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Pascal Schmidt, David Brandt, Tobias Busche, Joern Kalinowski
Summary: A method called ROSE was developed for characterizing bacterial promoters genome-wide using in vitro transcription coupled to transcriptome sequencing. ROSE identified 3226 transcription start sites in E. coli K-12 MG1655 genomic DNA, with 2167 also identified in in vivo studies and 598 being new. In vivo experiments confirmed that ROSE could identify repressed promoters not detected in in vivo experiments. Therefore, ROSE is a complementary method to study bacterial transcriptional networks and can identify promoters not captured by in vivo transcriptome studies.
Article
Plant Sciences
V. Miguel Palomar, Sarah Jaksich, Sho Fujii, Jan Kucinski, Andrzej T. Wierzbicki
Summary: In this study, the genome-wide pattern of plastid-encoded RNA polymerase (PEP) binding to chloroplast DNA was investigated using plastid chromatin immunoprecipitation-sequencing (ptChIP-seq) method. The results showed that PEP has a complex DNA binding pattern with preferential association at genes encoding rRNA, tRNA, and a subset of photosynthetic proteins in mature Arabidopsis thaliana chloroplasts. Sigma factors SIG2 and SIG6 were found to have effects on PEP binding to a subset of tRNA genes and throughout the rest of the genome. PEP binding was commonly enriched on gene promoters, around transcription start sites, and the levels of PEP binding to DNA were correlated with levels of RNA accumulation.
Article
Biochemical Research Methods
Nannan Zhao, Jie Song, Hao Zhang, Ying Lin, Shuangyan Han, Yuanyuan Huang, Suiping Zheng
Summary: The study identified and characterized a transcription factor-driven biosensor for putrescine and cadaverine in Corynebacterium glutamicum. By optimizing genetic components, the researchers obtained a highly sensitive variant and demonstrated its application in detecting putrescine in a C. glutamicum system.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Chirangini Pukhrambam, Vadim Molodtsov, Mahdi Kooshkbaghi, Ammar Tareen, Hoa Vu, Kyle S. Skalenko, Min Su, Zhou Yin, Jared T. Winkelman, Justin B. Kinney, Richard H. Ebright, Bryce E. Nickels
Summary: In sigma-dependent transcriptional pausing, the presence or absence of GreB determines whether the paused state involves backtracking or scrunched by 2-4 base pairs or 2-3 base pairs respectively. The consensus sequence T(-3)N(-2)Y(-1)G(+1) is associated with pausing in both initial transcription and transcription elongation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Ryo Kariyazono, Takashi Osanai
Summary: This study identified the binding sites of SigE and SigA using ChIP-seq analysis and found that they shared most of their binding sites, but SigE exclusively occupied the promoters of the SigE regulon.
Article
Cell Biology
Jimin Park, Harris H. Wang
Summary: The study investigates the relationship between sequence diversity and functional differences of primary sigma(70) factors in different bacteria, revealing significant fitness deficits across sigma(70) orthologs. This analysis provides insights to improve understanding of the evolution and engineering potential of this global regulator.
Article
Microbiology
Nadja A. Henke, Irene Krahn, Volker F. Wendisch
Summary: This study successfully achieved strong and overexpression of target genes by designing new expression vectors and combining two strategies, providing new possibilities for the development of biotechnology applications.
Article
Microbiology
Jan Blumenstein, Robert Radisch, Vaclav Stepanek, Michal Grulich, Hana Dostalova, Miroslav Patek
Summary: The bacterium Rhodococcus erythropolis CCM2595 has the ability to degrade toxic aromatic compounds, with its genes being controlled by sigma factors. Experiments have revealed the gene activation mechanism of R. erythropolis under various extreme conditions, providing insights into the complex stress responses induced by substances like phenol.
CURRENT MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Janne Purhonen, Anders Hofer, Jukka Kallijarvi
Summary: In this study, we developed a microplate assay based on real-time detection of the Broccoli RNA aptamer to quantify ribonucleoside triphosphates (rNTPs) in a non-specialized laboratory. The assay is specific and tolerant to concentrated tissue and cell extracts, making it an accurate method for quantifying rNTPs without the need for chromatography equipment.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Yang Liu, Wenzhi Yang, Tao Su, Chengchuan Che, Guizhi Li, Can Chen, Meiru Si
Summary: This study revealed that CssR in C. glutamicum mediates stress response through ligand-induced conformational changes of the protein, rather than cysteine oxidation-based thiol modification. CssR negatively controls the expression of the ncgl1576-ncgl1577 operon, its structural gene, and/or redox homeostasis-related genes, showing its crucial role in stress response.
MICROBIAL CELL FACTORIES
(2021)
Article
Multidisciplinary Sciences
Ruth M. Saecker, James Chen, Courtney E. Chiu, Brandon Malone, Johanna Sotiris, Mark Ebrahim, Laura Y. Yen, Edward T. Eng, Seth A. Darst
Summary: The initial step in gene expression requires opening the DNA duplex for RNA synthesis. Differences in DNA sequence and length upstream of the start site globally alter interactions between DNA and RNAP, impacting RPo lifetime and subsequent transcription steps. Limited sequence changes can trigger global alterations in the transcription bubble, modulating RPo lifetime and affecting the transcription cycle.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Yanting Duan, Weiji Zhai, Weijia Liu, Xiaomei Zhang, Jin-Song Shi, Xiaojuan Zhang, Zhenghong Xu
Summary: In this research, 17 core promoters and 29 RBSs in Corynebacterium glutamicum were characterized, showing significant differences in transcriptional and translational activity. The study revealed that RBSs contribute more to gene expression than promoters, but their efficacy is influenced by gene context, indicating poor orthogonality.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Liqiang Shen, Giorgio Lai, Linlin You, Jing Shi, Xiaoxian Wu, Maria Puiu, Zhanxi Gu, Yu Feng, Yulia Yuzenkova, Yu Zhang
Summary: This study presents the cryo-EM structures of cyanobacterial transcription initiation complexes, revealing the role of SI3-& sigma; arch interaction in transcription initiation of cyanobacteria. Disruption of this structure affects the growth and stress response of cyanobacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Cell Biology
Long Vo Ngoc, Torrey E. Rhyne, James T. Kadonaga
Summary: In this study, machine learning was used to compare DPR region, a DNA motif involved in transcription initiation, in humans and Drosophila. A distinct human-specific version of DPR was identified and machine learning models were used to predict synthetic DPR motifs with specificity for human transcription factors. These findings demonstrate the potential of machine learning in designing synthetic DNA elements with specific functional properties.
GENES & DEVELOPMENT
(2023)
Article
Thermodynamics
Helena Dolezalova-Weissmannova, Stanislav Maly, Martin Brtnicky, Jiri Holatko, Michael Scott Demyan, Christian Siewert, David Tokarski, Eliska Kamenikova, Jiri Kucerik
Summary: Thermogravimetry (TG) is a simple method for rapid analysis of soil properties, but its link with microbiological soil properties has not been systematically tested. This study aimed to search and validate the relationships between thermal mass losses (TML) and various soil properties. Results showed significant correlations between TML and basic soil properties, and equations developed from these correlations were successfully validated for prediction, mainly for arable soils.
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY
(2023)
Article
Environmental Sciences
Misha Iqbal, Muhammad Naveed, Muhammad Sanaullah, Martin Brtnicky, M. Iftikhar Hussain, Jiri Kucerik, Jiri Holatko, Adnan Mustafa
Summary: This study aims to investigate the influence of microorganisms such as Enterobacter sp., Bacillus sp., and Piriformospora indica on canola growth, and it was found that they can significantly improve canola biomass, root system, and yield.
JOURNAL OF SOILS AND SEDIMENTS
(2023)
Article
Environmental Sciences
Maja Radziemska, Aurelia Blazejczyk, Mariusz Z. Gusiatin, Agnieszka Cydzik-Kwiatkowska, Grzegorz Majewski, Tereza Hammerschmiedt, Wioletta Rogula-Kozlowska, Malgorzata Majder-Lopatka, Jiri Kucerik, Ayla Bilgin, Jiri Holatko, Antonin Kintl, Martin Brtnicky
Summary: The addition of natural zeolite to trace-element-contaminated soil can increase plant biomass and soil pH, and significantly decrease the total content of copper, lead, cadmium, and zinc in the soil, as well as the bioavailable and leachable content of these elements. Moreover, the presence of zeolite can also influence the bacterial diversity in the soil, favoring the growth of certain bacterial species with ecological importance.
LAND DEGRADATION & DEVELOPMENT
(2023)
Article
Chemistry, Physical
Jiri Holatko, Martin Brtnicky, Adnan Mustafa, Antonin Kintl, Petr Skarpa, Pavel Ryant, Tivadar Baltazar, Ondrej Malicek, Oldrich Latal, Tereza Hammerschmiedt
Summary: Digestate with amendments improves soil microbiological properties and provides plants with available nutrients. Addition of biochar and sulphur in digestate can significantly enhance the effects on soil health and plant biomass. Short-term and long-term fertilization effects were observed, with increased total nitrogen and carbon, as well as sulphur and arylsulfatase activity. However, no significant differences were observed in aboveground plant biomass.
Article
Energy & Fuels
Maja Radziemska, Mariusz Zygmunt Gusiatin, Zbigniew Mazur, Algirdas Radzevicius, Agnieszka Bes, Raimondas Sadzevicius, Jiri Holatko, Midona Dapkiene, Inga Adamonyte, Martin Brtnicky
Summary: The presence of potentially toxic elements (PTEs) in soils can be harmful to the natural balance and increase the risk of PTE incorporation into the food chain. Utilizing composite biochar and municipal sewage sludge compost (MSSC/C) can effectively manage waste and support phytostabilization processes. The study confirmed that the addition of MSSC/C to PTE-contaminated soil increased plant biomass, improved soil pH, and reduced PTE contents, particularly Cd, Cr, and Ni.
Article
Biochemistry & Molecular Biology
David Tuzincin, Petr Padrta, Hana Sanderova, Alzbeta Rabatinova, Katerina Bendova, Libor Krasny, Lukas Zidek, Pavel Kaderavek
Summary: Sigma factors are essential components of bacterial RNA polymerase and play a crucial role in recognizing promoter sequences and initiating transcription. In this study, it was found that domain 1.1 of Bacillus subtilis sigma(A) exists in structurally distinct variants in equilibrium, and the population of a minor unfolded state increases with temperature. Functional experiments revealed that the full-length sigma(A) increases transcription activity with temperature, while the version lacking domain 1.1 shows constant activity.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Jiri Holatko, Tereza Hammerschmiedt, Adnan Mustafa, Antonin Kintl, Petr Skarpa, Pavel Ryant, Tivadar Baltazar, Ondrej Malicek, Oldrich Latal, Martin Brtnicky
Summary: This study aimed to evaluate the differences in the effect of unenriched manure and manures co-matured with biochar, elemental sulfur or both amendments. The results showed that co-matured manure with biochar had the highest rate of maturation and significantly increased dry aboveground biomass weight in the half-time of the experiment. However, this effect vanished after 24 weeks. On the other hand, co-matured manure with biochar and elemental sulfur led to short-term carbon sequestration due to presumed retardation of microbial-mediated transformation of nutrients, increasing the recalcitrancy of soil organic matter and slowing down soil nutrient transformation.
SCIENTIFIC REPORTS
(2023)
Article
Plant Sciences
Tereza Hammerschmiedt, Jiri Holatko, Radim Zelinka, Antonin Kintl, Petr Skarpa, Zuzana Bytesnikova, Lukas Richtera, Adnan Mustafa, Ondrej Malicek, Martin Brtnicky
Summary: The impact of graphene oxide on soil properties is mixed, with both negative and positive effects. There are few studies on its single amendment to soil or in combination with nanosized sulfur. An eight-week pot experiment showed that graphene oxide had a positive effect on soil respiration, but its combination with high nano-sulfur had a negative effect on some types of respiration. Single application of graphene oxide enhanced arylsulfatase activity.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Environmental Sciences
Adnan Mustafa, Usman Zulfiqar, Muhammad Zahid Mumtaz, Maja Radziemska, Fasih Ullah Haider, Jiri Holatko, Tereza Hammershmiedt, Muhammad Naveed, Hassan Ali, Antonin Kintl, Qudsia Saeed, Jiri Kucerik, Martin Brtnicky
Summary: Scientists are interested in nickel (Ni) due to its essentiality and toxicity on terrestrial biota. It has been found that plants cannot complete their life cycle without an adequate supply of Ni. The safe limit of Ni for plants is 1.5 μg/g, and it plays crucial roles in various physiological functions.
Article
Agronomy
Jiri Holatko, Tereza Hammerschmiedt, Jiri Kucerik, Antonin Kintl, Tivadar Baltazar, Ondrej Malicek, Oldrich Latal, Martin Brtnicky
Summary: This research aimed to evaluate the effect of injecting digestate deeper into the soil profile of permanent grassland on soil and plant quality indicators. The results showed that the injector application of digestate improved long-term carbon sequestration, respiration, nitrate content, and urease activity. It also improved grass biomass yield and nutritional value, making it a viable agriculture management practice for digestate-based fertilisation of permanent grassland.
EUROPEAN JOURNAL OF AGRONOMY
(2023)
Article
Agronomy
Jakub Elbl, Antonin Kintl, Martin Brtnicky, Petr Sirucek, Jiri Mezera, Vladimir Smutny, Jan Vopravil, Jiri Holatko, Igor Hunady, Vojtech Lukas
Summary: This research investigates the impact of plot size changes on crop yield. The findings indicate that dividing plots into smaller parts increases the heterogeneity of crop yields and leads to an uneven distribution of yields. When dividing plots, higher yielding portions may accumulate in specific plots at the expense of others.
PLANT SOIL AND ENVIRONMENT
(2023)
Article
Environmental Sciences
Maja Radziemska, Mariusz Z. Gusiatin, Agnieszka Cydzik-Kwiatkowska, Aurelia Blazejczyk, Jiri Holatko, Martin Brtnicky
Summary: This article investigates the effect of a combined amendment, biochar+compost (BC), on the immobilization of Cd, Cu, Ni, Pb, and Zn in soil under freezing and thawing conditions (FTC). The study analyzes the speciation of these elements using sequential extraction and assesses the variability of the soil microbiome using 16S rRNA gene sequencing. The results show that BC promotes the biomass yield of L. perenne, but FTC decreases it. BC increases the content of heavy metals in plant roots and improves soil pH. BC has the greatest impact on increasing Cu stability by redistributing it from certain fractions to others. FTC affects the stability of heavy metals in the soil, especially for Pb and Zn. The core genera in the soil samples include Sphingomonas sp. and Mycobacterium sp., and FTC favors the growth of Bacteroidetes and Proteobacteria.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Agriculture, Multidisciplinary
Martin Brtnicky, Adnan Mustafa, Tereza Hammerschmiedt, Antonin Kintl, Lukas Trakal, Luke Beesley, Pavel Ryant, Carol Omara-Ojungu, Tivadar Baltazar, Jiri Holatko
Summary: This study investigates the effects of biochar application on soil microbial and plant parameters in agricultural soils. The results show that the addition of organic fertilizer with biochar significantly increases soil enzyme activity and plant biomass, while the activation of biochar reduces nutrient leaching from mineral fertilizers. Therefore, biochar has the potential to improve soil fertility and microbial activity in agriculture.
CHEMICAL AND BIOLOGICAL TECHNOLOGIES IN AGRICULTURE
(2023)
Article
Agronomy
Antonin Kintl, Igor Hunady, Tomas Vitez, Martin Brtnicky, Julie Sobotkova, Tereza Hammerschmiedt, Monika Vitezova, Jiri Holatko, Vladimir Smutny, Jakub Elbl
Summary: The study found that silages made from mixed cultures of legumes intercropped with maize are almost of the same or even better quality in terms of dry matter yield compared with pure maize silage. The addition of different legumes in mixed silages significantly affected the content of various nutrients, with some legumes increasing certain components such as lipids and others decreasing components like neutral detergent fiber and starch. Furthermore, the production of biogas from these mixed substrates was directly proportional to the content of certain nutrients, showing potential for sustainable biogas production.
Review
Microbiology
Petra Sudzinova, Hana Sanderova, Tomas Koval, Tereza Skalova, Nabajyoti Borah, Jarmila Hnilicova, Tomas Kouba, Jan Dohnalek, Libor Krasny
Summary: Rifampicin, a clinically important antibiotic, can bind to and block the DNA/RNA channel of bacterial RNA polymerase. HelR proteins from high G+C Actinobacteria have been found to dissociate rifampicin-stalled RNA polymerases from DNA, providing rifampicin resistance. This discovery provides a blueprint for studying novel mechanisms of bacterial antibiotic resistance.
FEMS MICROBIOLOGY REVIEWS
(2023)
