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- Behra, Phani Rama Krishna, et al.
(författare)
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Comparative genome analysis of Mycobacteria focusing on tRNA and non-coding RNA
- 2022
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Ingår i: BMC Genomics. - : BioMed Central (BMC). - 1471-2164. ; 23
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Mycobacterium genus encompasses at least 192 named species, many of which cause severe diseases such as tuberculosis. Non-tuberculosis mycobacteria (NTM) can also infect humans and animals. Some are of emerging concern because they show high resistance to commonly used antibiotics while others are used and evaluated in bioremediation or included in anticancer vaccines.Results: We provide the genome sequences for 114 mycobacterial type strains and together with 130 available mycobacterial genomes we generated a phylogenetic tree based on 387 core genes and supported by average nucleotide identity (ANI) data. The 244 genome sequences cover most of the species constituting the Mycobacterium genus. The genome sizes ranged from 3.2 to 8.1 Mb with an average of 5.7 Mb, and we identified 14 new plasmids. Moreover, mycobacterial genomes consisted of phage-like sequences ranging between 0 and 4.64% dependent on mycobacteria while the number of IS elements varied between 1 and 290. Our data also revealed that, depending on the mycobacteria, the number of tRNA and non-coding (nc) RNA genes differ and that their positions on the chromosome varied. We identified a conserved core set of 12 ncRNAs, 43 tRNAs and 18 aminoacyl-tRNA synthetases among mycobacteria.Conclusions; Phages, IS elements, tRNA and ncRNAs appear to have contributed to the evolution of the Mycobacterium genus where several tRNA and ncRNA genes have been horizontally transferred. On the basis of our phylogenetic analysis, we identified several isolates of unnamed species as new mycobacterial species or strains of known mycobacteria. The predicted number of coding sequences correlates with genome size while the number of tRNA, rRNA and ncRNA genes does not. Together these findings expand our insight into the evolution of the Mycobacterium genus and as such they establish a platform to understand mycobacterial pathogenicity, their evolution, antibiotic resistance/tolerance as well as the function and evolution of ncRNA among mycobacteria.
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| 2. |
- Behra, Phani Rama Krishna, et al.
(författare)
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Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Members of the Mycobacterium chelonae-abscessus complex (MCAC) are close to the mycobacterial ancestor and includes both human, animal and fish pathogens. We present the genomes of 14 members of this complex: the complete genomes of Mycobacterium salmoniphilum and Mycobacterium chelonae type strains, seven M. salmoniphilum isolates, and five M. salmoniphilum-like strains including strains isolated during an outbreak in an animal facility at Uppsala University. Average nucleotide identity (ANI) analysis and core gene phylogeny revealed that the M. salmoniphilum-like strains are variants of the human pathogen Mycobacterium franklinii and phylogenetically close to Mycobacterium abscessus. Our data further suggested that M. salmoniphilum separates into three branches named group I, II and III with the M. salmoniphilum type strain belonging to group II. Among predicted virulence factors, the presence of phospholipase C (plcC), which is a major virulence factor that makes M. abscessus highly cytotoxic to mouse macrophages, and that M. franklinii originally was isolated from infected humans make it plausible that the outbreak in the animal facility was caused by a M. salmoniphilum-like strain. Interestingly, M. salmoniphilum-like was isolated from tap water suggesting that it can be present in the environment. Moreover, we predicted the presence of mutational hotspots in the M. salmoniphilum isolates and 26% of these hotspots overlap with genes categorized as having roles in virulence, disease and defense. We also provide data about key genes involved in transcription and translation such as sigma factor, ribosomal protein and tRNA genes.
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| 3. |
- Das, Sarbashis, et al.
(författare)
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Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Mycobacterium marinum is the causative agent for the tuberculosis-like disease mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its geographical distribution, M. marinum is known to occupy diverse fish as hosts. However, information about its genomic diversity is limited. Here, we provide the genome sequences for 15 M. marinum strains isolated from infected humans and fish. Comparative genomic analysis of these and four available genomes of the M. marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the strains, leading to the conclusion that M. marinum should be divided into two different clusters, the "M"- and the "Aronson"-type. We suggest that these two clusters should be considered to represent two M. marinum subspecies. Our data also show that the M. marinum pan-genome for both groups is open and expanding and we provide data showing high number of mutational hotspots in M. marinum relative to other mycobacteria such as Mycobacterium tuberculosis. This high genomic diversity might be related to the ability of M. marinum to occupy different ecological niches.
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| 8. |
- Pettersson, B. M. Fredrik, 1974-, et al.
(författare)
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The Presence of a C− 1/G+ 73 Pair in a tRNA Precursor Influences Processing and Expression In Vivo
- 2008
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 381:5, s. 1089-1097
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Tidskriftsartikel (refereegranskat)abstract
- To understand whether 5′ and 3′ structural elements of the region corresponding to the mature tRNA affect the expression of the tRNA, we examined several bacterial genomes for tRNA genes where the expression might be potentially affected by structural elements located outside of the mature tRNA. In Pseudomonas aeruginosa, our analysis suggested that the tRNATrp is transcribed together with a putative stem–loop structure followed by a uridine tract immediately downstream of the tRNA region. This structural element, resembling a Rho-independent transcription terminator, might therefore influence the expression and processing of tRNATrp. Moreover, the secondary structure suggested that the discriminator base in the tRNATrp precursor can pair with either the C at position − 1, the 3′ terminal residue in the 5′ leader, or the C immediately 5′ of the uridine tract of the putative Rho-independent transcription terminator. Here, we present in vivo data demonstrating the importance of residue − 1 and the positioning of the putative transcription terminator for the expression of correctly 5′ processed P. aeruginosa tRNATrp in Escherichia coli. Interestingly, we also detected a difference in the appearance of correctly 5′ processed P. aeruginosa tRNATrp in E. coli compared to the situation in P. aeruginosa.
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| 10. |
- Pettersson, B. M. Fredrik, 1974-
(författare)
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tRNA Gene Structures in Bacteria
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In bacteria, tRNA molecules are produced as precursors with additional nucleotides both upstream and downstream of the tRNA coding sequence. To generate a mature tRNA, the endoribonuclease RNase P removes the upstream sequence, while a number of enzymes can remove the downstream sequence. In this thesis, the influence of such upstream and downstream sequences on the expression of mature functional tRNA was studied. It was found that in Escherichia coli, the presence of an upstream sequence positively influences tRNA expression. Furthermore, it was shown that the identity of the nucleotide immediatedly 5' of the canonical RNase P cleavage site in a tRNA precursor influenced RNase P cleavage site selection in vivo in E. coli, but not in Pseudomonas aeruginosa. Additionally, a stem-loop in the precursor just downstream of the tRNA increased this "miscleavage". This stem-loop resembled a rho-independent transcription terminator and overlapped the trpT gene in P. aeruginosa, but it only marginally influenced the expression of the downstream secE gene. The trpT and secE genes were found to be cotranscribed. The trpT-secE gene order was also conserved in the majority of bacteria investigated. The expression of tRNA genes during development in Streptomyces coelicolor was also studied. Here, the expression of most tRNA genes tested increased with time during development. Similarly, the expression of the RNase P RNA increased. The relative increase was quantified and correlated with different criteria related to gene structure and gene organisation, but no significant differences could be found. Moreover, a tRNALeuCAA UUA codon suppressor as well as the cognate bldA tRNA could restore differentiation to a developmentally blocked bldA deletion strain. For both tRNAs, the efficiency of restoration depended on the 5'- and 3'-flanks. In conclusion, both 5'- and 3'-flanking sequences influence tRNA expression, and bacteria respond differently to changes in their tRNA gene structures.
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