A5051040373- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- CRISPR and Genetic Engineering
- Bacteriophages and microbial interactions
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- SARS-CoV-2 and COVID-19 Research
- Genomics and Phylogenetic Studies
- Research on Leishmaniasis Studies
- Tuberculosis Research and Epidemiology
- Protein Structure and Dynamics
- Malaria Research and Control
- SARS-CoV-2 detection and testing
- Innovation and Socioeconomic Development
- Antimicrobial Resistance in Staphylococcus
- Plant-Microbe Interactions and Immunity
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Viral Infections and Immunology Research
- Fungal and yeast genetics research
- Protist diversity and phylogeny
- Antibiotic Resistance in Bacteria
- Bacterial biofilms and quorum sensing
- Plant Disease Resistance and Genetics
- Genomics and Chromatin Dynamics
- Biosensors and Analytical Detection
Lund University
2022-2024
Peruvian University of Applied Sciences
1957-2022
Universidad Peruana Cayetano Heredia
1957-2016
Toxin-antitoxin (TA) systems are a large group of small genetic modules found in prokaryotes and their mobile elements. Type II TAs encoded as bicistronic (two-gene) operons that encode two proteins: toxin neutralizing antitoxin. Using our tool NetFlax (standing for Network-FlaGs toxins antitoxins), we have performed large-scale bioinformatic analysis proteinaceous TAs, revealing interconnected clusters constituting core network TA-like gene pairs. To understand the structural basis...
Toxin-antitoxins (TAs) are prokaryotic two-gene systems composed of a toxin neutralized by an antitoxin. Toxin-antitoxin-chaperone (TAC) additionally include SecB-like chaperone that stabilizes the antitoxin recognizing its addiction (ChAD) element. TACs mediate antiphage defense, but mechanisms viral sensing and restriction unexplored. We identify two Escherichia coli TAC containing host inhibition growth (HigBA) CmdTA TA modules, HigBAC CmdTAC. is triggered through recognition gpV major...
During host colonization, bacteria use the alarmones (p)ppGpp to reshape their proteome by acting pleiotropically on DNA, RNA, and protein synthesis. Here, we elucidate how initiating ribosome senses cellular pool of guanosine nucleotides regulates progression towards Our results show that affinity triphosphate (GTP) inhibitory concentration ppGpp for 30S-bound initiation factor IF2 vary depending programmed mRNA. The TufA mRNA enhanced GTP 30S complexes, resulting in improved tolerance...
Tegumentary leishmaniasis, a disease caused by protozoan parasites of the genus Leishmania , is major public health problem in many regions Latin America. Its diagnosis difficult given other conditions resembling leishmaniasis lesions and co-occurring same endemic areas. A combination parasitological molecular methods leads to accurate diagnosis, with latter being traditionally performed centralized reference research laboratories as they require specialized infrastructure operators....
Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of can lethal, unless ribosomes are ArfA or ArfB alternative factors ribosome-associated quality control (RQC) system, which in Bacillus subtilis involves MutS2, RqcH, RqcP Pth. Using transposon sequencing a trans-translation-incompetent B. strain we identify poorly...
HflX is a ubiquitous bacterial GTPase that splits and recycles stressed ribosomes. In addition to HflX, Listeria monocytogenes contains second homolog, HflXr. Unlike HflXr confers resistance macrolide lincosamide antibiotics by an experimentally unexplored mechanism. Here, we have determined cryo-EM structures of L. HflXr-50S HflX-50S complexes as well 70S ribosomes in the presence absence lincomycin. While overall geometry on 50S subunit similar loop within N-terminal domain HflXr, which...
Bacterial translation initiation factor IF3 is composed of two distinct domains, a well-characterized C-terminal domain (IF3C), which enhances the speed and fidelity initiation, less understood N-terminal (IF3N). In this study, we developed an aptamer (Apt343) that targets IF3N with goal elucidating its contribution to initiation. Rapid kinetics assays revealed Apt343 reduces rate association 30S ribosomal subunit by 13-fold, while inducing pronounced rearrangement both domains on 30S. These...
Aminoglycoside antibiotics are widely used to treat infectious diseases. Among them, streptomycin and kanamycin (and derivatives) of importance battle multidrug-resistant (MDR) Mycobacterium tuberculosis. Both drugs bind the small ribosomal subunit (30S) inhibit protein synthesis. Genetic, structural, biochemical studies indicate that local long-range conformational rearrangements 30S account for this inhibition. Here, we use intramolecular FRET between C- N-terminus domains flexible IF3...
Rapid Diagnostic Tests (RDTs) for malaria are restricted to a few biomarkers and antibody-mediated detection. However, the expression of commonly used varies geographically sensibility immunodetection can be affected by batch-to-batch differences or limited thermal stability. In this study we aimed overcome these limitations identifying potential biomarker developing molecular sensors based on aptamer technology. Using gene databases, ribosome profiling analysis, structural modeling, find...
Abstract Initiation factor IF3 is an essential protein that enhances the fidelity and speed of bacterial mRNA translation initiation. Here, we describe dynamic interplay between domains their alternative binding sites using pre-steady state kinetics combined with molecular modelling available structures initiation complexes. Our results show accommodates its at velocities ranging over two orders magnitude, responding to each 30S ligand. IF1 IF2 promote compaction movement C-terminal domain...
Abstract Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of can lethal, unless ribosomes are ArfA or ArfB alternative factors ribosome-associated quality control (RQC) system, which in B. subtilis involves MutS2, RqcH, RqcP Pth. Using transposon sequencing a trans-translation-incompetent strain we identify poorly...
Toxin-antitoxin (TA) systems are a large group of small genetic modules found in prokaryotes and their mobile elements. Type II TAs encoded as bicistronic (two-gene) operons that encode two proteins: toxin neutralising antitoxin. Using our tool NetFlax (standing for Network-FlaGs toxins antitoxins) we have performed large-scale bioinformatic analysis proteinaceous TAs, revealing interconnected clusters constituting core network TA-like gene pairs. To understand the structural basis...
Here, we describe a detailed step-by-step protocol to detect SARS-CoV-2 RNA using RT-PCR-mediated amplification and CRISPR/Cas-based visualization. The optimized assay uses basic molecular biology equipment such as conventional thermocyclers transilluminators for qualitative detection. Alternatively, fluorescence plate reader can be used quantitative measurements. detects two regions of the genome in addition human RNaseP sample control. Aiming reach remote regions, this work was developed...
Here, we describe a detailed step-by-step protocol for the expression, purification, quantification, and activity determination of key enzymes molecular detection pathogens. Based on previous reports, optimized LbCas12a, Taq DNA polymerase, M-MLV reverse transcriptase, TEV protease to make it compatible with minimal laboratory equipment, broadly available in low- middle-income countries. The produced this have been successfully used applications. For complete details use execution protocol,...
During nutrient limitation, bacteria produce the alarmones (p)ppGpp as effectors of a stress signaling network termed stringent response. RsgA, RbgA, Era, and HflX are four ribosome-associated GTPases (RA-GTPases) that bind to in Staphylococcus aureus. These enzymes cofactors ribosome assembly, where they cycle between ON (GTP-bound) OFF (GDP-bound) states. Entry into state occurs upon hydrolysis GTP, with GTPase activity increasing substantially association. When bound (p)ppGpp, is...
Journal Article The native ABC-F proteins of Staphylococcus aureus do not contribute to intrinsic resistance against ribosome-targeting antibacterial drugs Get access Luiza H Galarion, Galarion Faculty Biological Sciences, School Molecular and Cellular Biology, University Leeds, Leeds LS2 9JT, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar James Trigwell, Trigwell Merianne Mohamad, Mohamad Jose A Nakamoto, Nakamoto Department Experimental Medical Science,...
Abstract Tegumentary leishmaniasis, a disease caused by protozoan parasites of the genus Leishmania , is major public health problem in many regions Latin America. Its diagnosis difficult given other conditions resembling leishmaniasis lesions and co-occurring same endemic areas. A combination parasitological molecular methods lead to accurate diagnosis, with latter being traditionally performed centralized reference research laboratories as they require specialized infrastructure operators....
Summary Toxin-antitoxins (TAs) are prokaryotic two-gene systems comprised of a toxin neutralised by an antitoxin. Toxin-antitoxin-chaperone (TAC) additionally include SecB-like chaperone that stabilises the antitoxin recognising its addiction (ChAD) element. TACs have been shown to mediate antiphage defence, but mechanisms viral sensing and restriction unexplored. We identify characterise two Escherichia coli TAC containing HigBA CmdTA TA units, HigBAC CmdTAC. The is triggered through...
Abstract Rapid Diagnostic Tests (RDTs) for malaria are restricted to a few biomarkers and antibody-mediated detection. However, the expression of commonly used varies geographically sensibility immunodetection can be affected by batch-to-batch differences or limited thermal stability. In this study we aimed overcome these limitations identifying potential biomarker developing molecular sensors based on aptamer technology. Using gene databases, ribosome profiling analysis, structural...
Abstract Initiation factor 3 (IF3) is an essential protein that enhances the fidelity and speed of bacterial initiation mRNA translation. The dynamic interplay between two independent IF3 domains, their alternative binding sites, mechanism ensures translation remains elusive. Here, we show functional positioning domains occurs at velocities ranging over orders magnitude, driven by each 30S ligand. IF1 IF2 rapidly promote accommodation on platform with C-terminal domain moving towards P site....
ABSTRACT During nutrient limitation, bacteria produce the alarmones (p)ppGpp as effectors of stress signalling network termed stringent response. Screening for (p)ppGpp-binding targets within Staphylococcus aureus identified four ribosome-associated GTPases (RA-GTPases), RsgA, RbgA, Era and HflX, each which are cofactors in ribosome assembly, where they cycle between ON (GTP-bound) OFF (GDP-bound) states. Entry into OFF-state from ON-state occurs upon hydrolysis GTP, with GTPase activity...
Abstract The testis-determining factor (TDF) is an essential transcriptional protein for male differentiation in mammals, expressed along spermatids to early zygotes and, some extent, diverse cellular lines. In this study, we developed fluorescent biosensors capable of indicating the presence TDF. We used vitro evolution techniques produce RNA aptamers that bind recombinantly HMG-box, DNA binding domain Bioinformatic analysis setup suggested two predominant aptamer clusters with distinctive...