| 1. |
- Avican, Kemal, et al.
(författare)
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RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial processes necessary for adaption to stressful host environments are potential targets for new antimicrobials. Here, we report large-scale transcriptomic analyses of 32 human bacterial pathogens grown under 11 stress conditions mimicking human host environments. The potential relevance of the in vitro stress conditions and responses is supported by comparisons with available in vivo transcriptomes of clinically important pathogens. Calculation of a probability score enables comparative cross-microbial analyses of the stress responses, revealing common and unique regulatory responses to different stresses, as well as overlapping processes participating in different stress responses. We identify conserved and species-specific ‘universal stress responders’, that is, genes showing altered expression in multiple stress conditions. Non-coding RNAs are involved in a substantial proportion of the responses. The data are collected in a freely available, interactive online resource (PATHOgenex).
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| 2. |
- Negeri, Abebe Aseffa, et al.
(författare)
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Antimicrobial Resistance Profiling and Molecular Epidemiological Analysis of Extended Spectrum β-Lactamases Produced by Extraintestinal Invasive Escherichia coli Isolates From Ethiopia : The Presence of International High-Risk Clones ST131 and ST410 Revealed
- 2021
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- The treatment of invasive Escherichia coli infections is a challenge because of the emergence and rapid spread of multidrug resistant strains. Particular problems are those strains that produce extended spectrum β-lactamases (ESBL's). Although the global characterization of these enzymes is advanced, knowledge of their molecular basis among clinical E. coli isolates in Ethiopia is extremely limited. This study intends to address this knowledge gap. The study combines antimicrobial resistance profiling and molecular epidemiology of ESBL genes among 204 E. coli clinical isolates collected from patient urine, blood, and pus at four geographically distinct health facilities in Ethiopia. All isolates exhibited multidrug resistance, with extensive resistance to ampicillin and first to fourth line generation cephalosporins and sulfamethoxazole-trimethoprim and ciprofloxacin. Extended spectrum β-lactamase genes were detected in 189 strains, and all but one were positive for CTX-Ms β-lactamases. Genes encoding for the group-1 CTX-Ms enzymes were most prolific, and CTX-M-15 was the most common ESBL identified. Group-9 CTX-Ms including CTX-M-14 and CTX-27 were detected only in 12 isolates and SHV ESBL types were identified in just 8 isolates. Bacterial typing revealed a high amount of strains associated with the B2 phylogenetic group. Crucially, the international high risk clones ST131 and ST410 were among the sequence types identified. This first time study revealed a high prevalence of CTX-M type ESBL's circulating among E. coli clinical isolates in Ethiopia. Critically, they are associated with multidrug resistance phenotypes and high-risk clones first characterized in other parts of the world.
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| 3. |
- Karlsborn, Tony, et al.
(författare)
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Elongator, a conserved complex required for wobble uridine modifications in Eukaryotes
- 2014
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Ingår i: RNA Biology. - : Taylor & Francis. - 1547-6286 .- 1555-8584. ; 11:12, s. 1519-1528
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Tidskriftsartikel (refereegranskat)abstract
- Elongator is a 6 subunit protein complex highly conserved in eukaryotes. The role of this complex has been controversial as the pleiotropic phenotypes of Elongator mutants have implicated the complex in several cellular processes. However, in yeast there is convincing evidence that the primary and probably only role of this complex is in formation of the 5-methoxycarbonylmethyl (mcm(5)) and 5-carbamoylmethyl (ncm(5)) side chains on uridines at wobble position in tRNA. In this review we summarize the cellular processes that have been linked to the Elongator complex and discuss its role in tRNA modification and regulation of translation. We also describe additional gene products essential for formation of ncm(5) and mcm(5) side chains at U-34 and their influence on Elongator activity.
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| 4. |
- Karlsborn, Tony, 1987-, et al.
(författare)
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Loss of ncm5 and mcm5 wobble uridine side chains results in an altered metabolic profile
- 2016
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Ingår i: Metabolomics. - : Springer. - 1573-3882 .- 1573-3890. ; 12:12
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: The Elongator complex, comprising six subunits (Elp1p-Elp6p), is required for formation of 5-carbamoylmethyl (ncm(5)) and 5-methoxycarbonylmethyl (mcm(5)) side chains on wobble uridines in 11 out of 42 tRNA species in Saccharomyces cerevisiae. Loss of these side chains reduces the efficiency of tRNA decoding during translation, resulting in pleiotropic phenotypes. Overexpression of hypomodified tRNA(s2UUU)(Lys); tRNA(s2UUG)(Gln) and tRNA(s2UUC)(Glu), which in wild-type strains are modified with mcm(5)s(2)U, partially suppress phenotypes of an elp3 Delta strain. Objectives: To identify metabolic alterations in an elp3 Delta strain and elucidate whether these metabolic alterations are suppressed by overexpression of hypomodified tRNA(s2UUU)(Lys); tRNA(s2UUG)(Gln) and tRNA(s2UUC)(Glu). Method: Metabolic profiles were obtained using untargeted GC-TOF-MS of a temperature-sensitive elp3 Delta strain carrying either an empty low-copy vector, an empty high-copy vector, a low-copy vector harboring the wild-type ELP3 gene, or a high-copy vector overexpressing tRNA(s2UUU)(Lys); tRNA(s2UUG)(Gln) and tRNA(s2UUC)(Glu). The temperature sensitive elp3 Delta strain derivatives were cultivated at permissive (30 degrees C) or semi-permissive (34 degrees C) growth conditions. Results: Culturing an elp3 Delta strain at 30 or 34 degrees C resulted in altered metabolism of 36 and 46 %, respectively, of all metabolites detected when compared to an elp3D strain carrying the wild-type ELP3 gene. Overexpression of hypomodified tRNA(s2UUU)(Lys); tRNA(s2UUG)(Gln) and tRNA(s2UUC)(Glu) suppressed a subset of the metabolic alterations observed in the elp3 Delta strain. Conclusion: Our results suggest that the presence of ncm(5)- and mcm(5)-side chains on wobble uridines in tRNA are important for metabolic homeostasis.
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| 5. |
- Mahmud, A. K. M. Firoj, et al.
(författare)
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A core transcriptional response for biofilm formation by Y. pseudotuberculosis
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Previous transcriptional profiling of the enteropathogen Yersinia pseudotuberculosis during persistent stages of colonisation of mouse cecal lymphoid follicles indicated the possible involvement of biofilm in infection maintenance. Not much is known about the mechanisms responsible for biofilm formation by this pathogen, and most current knowledge is based on results of experiments conducted using the related Y. pestis pathogen that forms biofilm in the flea gut. In this study, we performed transcriptional profiling of Y. pseudotuberculosis in biofilms from different biofilm-inducing conditions, bile exposure, amino acid deprivation and in vivo mimicking conditions with and without oxygen. The comparison of differential expression of genes in biofilm versus planktonic bacteria showed a set of 54 core genes that were similarly regulated, independent of inducing condition. This set included many genes that were previously shown to be associated with biofilms, such as hutG, hsmF, hmsT and cpxP that were upregulated and other genes such as hmsP and rfaH that were downregulated. There were also novel biofilm-associated genes, including genes encoding hypothetical proteins. To identify the genes involved in inducing biofilm formation, the gene expression of bacteria during an early initial phase when biofilm starts to form after induction by bile or amino acid depletion was determined. Comparisons of the resulting gene expression profiles with the profiles of non-induced bacteria incubated for the same period of time showed a set of core genes associated with early biofilm formation. This set included genes involved in quorum sensing, pili biogenesis and genes indicative of a potential metabolic shift involving nitrogen utilisation. Genes encoding components of sugar phosphotransferase systems were also upregulated during biofilm induction. Assays of biofilm formation by bacteria deleted of some of these core genes showed that strains lacking hpr and luxS, which are known to be important for functional sugar phosphotransferase systems and quorum sensing, as well as glnL encoding a sensory histidine kinase were most negatively affected. Most of the deletion mutant strains tested were affected, but the effect was less severe, suggesting high levels of redundancy in the pathways involved in biofilm formation by this pathogen.
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| 6. |
- Mahmud, A. K. M. Firoj, et al.
(författare)
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Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules
- 2020
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Ingår i: Journal of Computational Biology. - : Mary Ann Liebert. - 1066-5277 .- 1557-8666. ; 27:8, s. 1313-1328
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Tidskriftsartikel (refereegranskat)abstract
- Multiple transcription factors (TFs) bind to specific sites in the genome and interact among themselves to form the cis-regulatory modules (CRMs). They are essential in modulating the expression of genes, and it is important to study this interplay to understand gene regulation. In the present study, we integrated experimentally identified TF binding sites collected from published studies with computationally predicted TF binding sites to identifyDrosophilaCRMs. Along with the detection of the previously known CRMs, this approach identified novel protein combinations. We determined high-occupancy target sites, where a large number of TFs bind. Investigating these sites revealed that Giant, Dichaete, and Knirp are highly enriched in these locations. A common TAG team motif was observed at these sites, which might play a role in recruiting other TFs. While comparing the binding sites at distal and proximal promoters, we found that certain regulatory TFs, such as Zelda, were highly enriched in enhancers. Our study has shown that, from the information available concerning the TF binding sites, the real CRMs could be predicted accurately and efficiently. Although we only may claim co-occurrence of these proteins in this study, it may actually point to their interaction (as known interaction proteins typically co-occur together). Such an integrative approach can, therefore, help us to provide a better understanding of the interplay among the factors, even though further experimental verification is required.
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| 7. |
- Mahmud, A. K. M. Firoj, et al.
(författare)
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Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis
- 2020
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Ingår i: mSystem. - 2379-5077. ; 5:6
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Tidskriftsartikel (refereegranskat)abstract
- RpoN, an alternative sigma factor commonly known as σ54, is implicated in persistent stages of Yersinia pseudotuberculosis infections in which genes associated with this regulator are upregulated. We here combined phenotypic and genomic assays to provide insight into its role and function in this pathogen. RpoN was found essential for Y. pseudotuberculosis virulence in mice, and in vitro functional assays showed that it controls biofilm formation and motility. Mapping genome-wide associations of Y. pseudotuberculosis RpoN using chromatin immunoprecipitation coupled with next-generation sequencing identified an RpoN binding motif located at 103 inter- and intragenic sites on both sense and antisense strands. Deletion of rpoN had a large impact on gene expression, including downregulation of genes encoding proteins involved in flagellar assembly, chemotaxis, and quorum sensing. There were also clear indications of cross talk with other sigma factors, together with indirect effects due to altered expression of other regulators. Matching differential gene expression with locations of the binding sites implicated around 130 genes or operons potentially activated or repressed by RpoN. Mutagenesis of selected intergenic binding sites confirmed both positive and negative regulatory effects of RpoN binding. Corresponding mutations of intragenic sense sites had less impact on associated gene expression. Surprisingly, mutating intragenic sites on the antisense strand commonly reduced expression of genes carried by the corresponding sense strand.
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| 8. |
- Mahmud, A. K. M. Firoj, 1980-
(författare)
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Molecular mechanisms of Yersinia pseudotuberculosis for adaptation and establishment of infection in host tissue
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Bacterial pathogens can evade the host’s immune defence to adapt and establish an infection within the host. Some even slip into a quiescent state to establish themselves without acutely harming the host. Phylogenetically unrelated bacteria can share similar strategies for the establishment of infection and for persistence. Our lab previously showed that Yersinia pseudotuberculosis underwent a dramatic reprogramming from a virulent phenotype expressing virulence genes, including T3SS and Yop effectors during early infection, to an adapted phenotype capable of persisting in tissue. The overall aim of my PhD study was to dissect the mechanisms behind bacterial adaptation and maintenance of infection within host tissue using Y. pseudotuberculosis as a model pathogen. The ultimate goal is to identify key players of critical importance for the ability of the bacterium to maintain and establish infection in host tissue. In my studies, I mainly focused on bacterial biofilm and the role of the alternative sigma factor RpoN. Much of my studies involve RNA-Seq analyses, encouraging me to develop a convenient, time-efficient, and all-purpose RNA-Seq data analysis package especially designed for prokaryotic organisms. The package is available online as a free tool and can be used by any biologist with minimal computational knowledge. We systematically examined biofilm formation of Y. pseudotuberculosis under different stress conditions and found that biofilm development involved a series of adaptive responses against various stressors, including bile, pH, amino acid deprivation, and temperature and oxygen-level changes. Analyses of transcription profiles of bacteria forming biofilm in different conditions revealed a set of core genes that were similarly regulated in biofilm bacteria independently of induced environment. The transcriptional regulator RpoN, commonly known as sigma 54, was found to be important for biofilm formation, and a ∆rpoN mutant strain was severely attenuated in virulence. To understand the regulatory mechanisms involved, we investigated gene expressions in wild-type (WT) and the isogenic ∆rpoN mutant strain and also chromatin immunoprecipitation followed by sequencing. We have identified RpoN binding sites in the Y. pseudotuberculosis genome and revealed a complex regulation by RpoN involving both activation and repression effects. We also investigated the role of RpoN in regulation of the Type III secretion system (T3SS) and found that RpoN was required for a functional T3SS, which is essential for bacterial virulence properties in host tissue. Our work indicates that Yersinia modulates itself in multiple ways to create niches favourable to growth and survival in the host environment. We have identified some key regulators and genes that will be explored further for their potential as novel targets for the development of new antibiotics.
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| 9. |
- Mahmud, A. K. M. Firoj, et al.
(författare)
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ProkSeq for complete analysis of RNA-Seq data from prokaryotes
- 2021
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Ingår i: Bioinformatics. - UK : Oxford University Press. - 1367-4803 .- 1367-4811 .- 1460-2059. ; 37:1, s. 126-128
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Tidskriftsartikel (refereegranskat)abstract
- Summary: Since its introduction, RNA-Seq technology has been used extensively in studies of pathogenic bacteria to identify and quantify differences in gene expression across multiple samples from bacteria exposed to different conditions. With some exceptions, tools for studying gene expression, determination of differential gene expression, downstream pathway analysis and normalization of data collected in extreme biological conditions is still lacking. Here, we describe ProkSeq, a user-friendly, fully automated RNA-Seq data analysis pipeline designed for prokaryotes. ProkSeq provides a wide variety of options for analysing differential expression, normalizing expression data and visualizing data and results.Availability and implementation: ProkSeq is implemented in Python and is published under the MIT source license. The pipeline is available as a Docker container https://hub.docker.com/repository/docker/snandids/prokseq-v2.0, or can be used through Anaconda: https://anaconda.org/snandiDS/prokseq. The code is available on Github: https://github.com/snandiDS/prokseq and a detailed user documentation, including a manual and tutorial can be found at https://prokseqV20.readthedocs.io.
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| 10. |
- Mahmud, A. K. M. Firoj, et al.
(författare)
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RpoN is required for a functional type III secretion system in Yersinia pseudotuberculosis
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Pathogenic bacteria use a broad range of virulence factors to successfully thrive within their host. Yersinia pseudotuberculosis, a gram-negative enteropathogen of humans, utilises a type III secretion system (T3SS) to overcome the host’s innate immune response. T3SS gene expression is influenced by RpoN, a global regulator that has been shown to be essential for virulence in Y. pseudotuberculosis. To gain further insight into the link between RpoN and T3SS gene expression, we employed different approaches, such as time-course transcriptome profiling, sigma factor overexpression, binding site point mutation and protein secretion analyses. Our findings suggest that the RpoN-mediated effect on T3SS gene expression is multifactorial with sigma factor cross-talk involving effects on transcription of the yscNU operon.
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