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Kirsebom, Leif
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Publications (10 of 22) Show all publications
Mao, G., Srivastava, A. S., Wu, S., Kosek, D., Lindell, M. & Kirsebom, L. (2018). Critical domain interactions for type A RNase P RNA catalysis with and without the specificity domain. PLoS ONE, 13(3), Article ID e0192873.
Open this publication in new window or tab >>Critical domain interactions for type A RNase P RNA catalysis with and without the specificity domain
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2018 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 3, article id e0192873Article in journal (Refereed) Published
Abstract [en]

The natural trans-acting ribozyme RNase P RNA (RPR) is composed of two domains in which the catalytic (C-) domain mediates cleavage of various substrates. The C-domain alone, after removal of the second specificity (S-) domain, catalyzes this reaction as well, albeit with reduced efficiency. Here we provide experimental evidence indicating that efficient cleavage mediated by the Escherichia coli C-domain (Eco CP RPR) with and without the C5 protein likely depends on an interaction referred to as the "P6-mimic". Moreover, the P18 helix connects the C-and S-domains between its loop and the P8 helix in the S-domain (the P8/P18-interaction). In contrast to the "P6-mimic", the presence of P18 does not contribute to the catalytic performance by the C-domain lacking the S-domain in cleavage of an all ribo model hairpin loop substrate while deletion or disruption of the P8/P18-interaction in full-size RPR lowers the catalytic efficiency in cleavage of the same model hairpin loop substrate in keeping with previously reported data using precursor tRNAs. Consistent with that P18 is not required for cleavage mediated by the C-domain we show that the archaeal Pyrococcus furiosus RPR C-domain, which lacks the P18 helix, is catalytically active in trans without the S-domain and any protein. Our data also suggest that the S-domain has a larger impact on catalysis for E. coli RPR compared to P. furiosus RPR. Finally, we provide data indicating that the absence of the S-domain and P18, or the P8/P18-interaction in full-length RPR influences the charge distribution near the cleavage site in the RPR-substrate complex to a small but reproducible extent.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-350629 (URN)10.1371/journal.pone.0192873 (DOI)000426813200007 ()29509761 (PubMedID)
Funder
Swedish Research Council, 621-2011-5848Swedish Research Council, 2016-04602Swedish Research Council, 349-2008-6593
Available from: 2018-05-21 Created: 2018-05-21 Last updated: 2018-05-21Bibliographically approved
Das, S., Pettersson, B. M., Behra, P. R., Ramesh, M., Dasgupta, S., Bhattacharya, A. & Kirsebom, L. A. (2016). The Mycobacterium phlei Genome: Expectations and Surprises. Genome Biology and Evolution, 8(4), 975-985
Open this publication in new window or tab >>The Mycobacterium phlei Genome: Expectations and Surprises
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2016 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 8, no 4, p. 975-985Article in journal (Refereed) Published
Abstract [en]

Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 1898-1899. We present the complete genome sequence for the IV, phlei CCUG21000(T) type strain and the draft genomes for four additional strains. The genome size for all five is 5.3 Mb with 69.4% Guanine-Cytosine content. This is approximate to 0.35 Mbp smaller than the previously reported M. phlei RIVM draft genome. The size difference is attributed partly to large bacteriophage sequence fragments in the M. phlei RIVM genome. Comparative analysis revealed the following: 1) A CRISPR system similar to Type 1E (cas3) in M. phiei RIVM; 2) genes involved in polyamine metabolism and transport (potAD, potT) that are absent in other mycobacteria, and 3) strain specific variations in the number of sigma-factor genes. Moreover, M. phlei has as many as 82 mce (mammalian cell entry) homologs and many of the horizontally acquired genes in M. phlei are present in other environmental bacteria including mycobacteria that share similar habitat. Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and Mycobacterium rhodesiae NBB3, while it is more distant to M. smegmatis mc2 155.

Keywords
Mycobacterium phlei genome sequence, mycobacterial growth, comparative genome analysis, mycobacterial phylogeny
National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-298249 (URN)10.1093/gbe/evw049 (DOI)000376126400002 ()26941228 (PubMedID)
Funder
Swedish Research CouncilSida - Swedish International Development Cooperation AgencySwedish Research Council FormasSwedish National Infrastructure for Computing (SNIC), b2011072
Available from: 2016-07-01 Created: 2016-07-01 Last updated: 2018-01-10Bibliographically approved
Das, S., Pettersson, B. M., Behra, P. R., Ramesh, M., Dasgupta, S., Bhattacharya, A. & Kirsebom, L. A. (2015). Characterization of three Mycobacterium spp. with potential use in bioremediation by genome sequencing and comparative genomics. Genome Biology and Evolution, 7(7), 1871-1886
Open this publication in new window or tab >>Characterization of three Mycobacterium spp. with potential use in bioremediation by genome sequencing and comparative genomics
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2015 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 7, no 7, p. 1871-1886Article in journal (Refereed) Published
Abstract [en]

We provide the genome sequences of the type strains of the polychlorophenol-degrading Mycobacterium chlorophenolicum (DSM43826), the degrader of chlorinated aliphatics Mycobacterium chubuense (DSM44219) and Mycobacterium obuense (DSM44075) that has been tested for use in cancer immunotherapy. The genome sizes of M. chlorophenolicum, M. chubuense and M. obuense are 6.93, 5.95 and 5.58 Mbps with GC-contents of 68.4, 69.2 and 67.9%, respectively. Comparative genomic analysis revealed that 3254 genes are common and we predicted approximately 250 genes acquired through horizontal gene transfer from different sources including proteobacteria. The data also showed that the biodegrading Mycobacterium spp. NBB4, also referred to as M. chubuense NBB4, is distantly related to the M. chubuense type strain and should be considered as a separate species, we suggest it to be named M. ethylenense NBB4. Among different categories we identified genes with potential roles in: biodegradation of aromatic compounds, and copper homeostasis. These are the first non-pathogenic Mycobacterium spp. found harboring genes involved in copper homeostasis. These findings would therefore provide insight into the role of this group of Mycobacterium spp. in bioremediation as well as the evolution of copper homeostasis within the Mycobacterium genus.

National Category
Bioremediation
Identifiers
urn:nbn:se:uu:diva-257688 (URN)10.1093/gbe/evv111 (DOI)000358800500003 ()26079817 (PubMedID)
Available from: 2015-07-07 Created: 2015-07-07 Last updated: 2017-12-04Bibliographically approved
Pettersson, B. M., Das, S., Behra, P. R., Jordan, H. R., Ramesh, M., Mallick, A., . . . Kirsebom, L. A. (2015). Comparative Sigma Factor-mRNA Levels in Mycobacterium marinum under Stress Conditions and during Host Infection. PLoS ONE, 10(10), Article ID e0139823.
Open this publication in new window or tab >>Comparative Sigma Factor-mRNA Levels in Mycobacterium marinum under Stress Conditions and during Host Infection
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2015 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 10, article id e0139823Article in journal (Refereed) Published
Abstract [en]

We have used RNASeq and qRT-PCR to study mRNA levels for all s-factors in different Mycobacterium marinum strains under various growth and stress conditions. We also studied their levels in M. marinum from infected fish and mosquito larvae. The annotated s-factors were expressed and transcripts varied in relation to growth and stress conditions. Some were highly abundant such as sigA, sigB, sigC, sigD, sigE and sigH while others were not. The s-factor mRNA profiles were similar after heat stress, during infection of fish and mosquito larvae. The similarity also applies to some of the known heat shock genes such as the a-crystallin gene. Therefore, it seems probable that the physiological state of M. marinum is similar when exposed to these different conditions. Moreover, the mosquito larvae data suggest that this is the state that the fish encounter when infected, at least with respect to s-factor mRNA levels. Comparative genomic analysis of s-factor gene localizations in three M. marinum strains and Mycobacterium tuberculosis H37Rv revealed chromosomal rearrangements that changed the localization of especially sigA, sigB, sigD, sigE, sigF and sigJ after the divergence of these two species. This may explain the variation in species-specific expression upon exposure to different growth conditions.

National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-265822 (URN)10.1371/journal.pone.0139823 (DOI)000362510600087 ()26445268 (PubMedID)
Funder
Swedish Research Council
Available from: 2015-11-03 Created: 2015-11-03 Last updated: 2017-12-01Bibliographically approved
Herrmann, B., Stolt, P., Abdeldaim, G., Rubin, C.-J., Kirsebom, L. A. & Thollesson, M. (2014). Differentiation and Phylogenetic Relationships in Mycobacterium spp with Special Reference to the RNase P RNA Gene rnpB. Current Microbiology, 69(5), 634-639
Open this publication in new window or tab >>Differentiation and Phylogenetic Relationships in Mycobacterium spp with Special Reference to the RNase P RNA Gene rnpB
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2014 (English)In: Current Microbiology, ISSN 0343-8651, E-ISSN 1432-0991, Vol. 69, no 5, p. 634-639Article in journal (Refereed) Published
Abstract [en]

The rnpB gene encodes for the RNA subunit of the catalytic ribonuclease RNase P and is present in all bacteria and has both conserved and highly variable sequence regions. Determination of rnpB in 35 Mycobacterium spp. showed species specific sequences for all species except the Mycobacterium tuberculosis complex (four species). High sequence variation was seen in the P3, P15 and P19 regions of suggested secondary structures of the corresponding RNase P RNA molecules. Phylogenetic analysis showed that rnpB gave similar tree topologies as 16S rRNA and hsp65 genes. A combined analysis of the three genes increased the number of nodes with significant support from 10 to 19. The results indicate that rnpB is useful for phylogenetic studies and is a possible target for identification and detection of Mycobacterium spp.

National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-237900 (URN)10.1007/s00284-014-0630-8 (DOI)000343913500007 ()24962595 (PubMedID)
Available from: 2014-12-11 Created: 2014-12-08 Last updated: 2017-12-05Bibliographically approved
Gößringer, M., Helmecke, D., Köhler, K., Schön, A., Kirsebom, L. A., Bindereif, A. & Hartmann, R. K. (2014). Enzymatic RNA Synthesis Using Bacteriophage T7 RNA Polymerase (2ed.). In: Roland K. Hartmann, Albrecht Bindereif, Astrid Schön, Eric Westhof (Ed.), Handbook of RNA Biochemistry: Second, Completely Revised and Enlarged Edition (pp. 1-28). Weinheim: Wiley-Blackwell, 1-2
Open this publication in new window or tab >>Enzymatic RNA Synthesis Using Bacteriophage T7 RNA Polymerase
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2014 (English)In: Handbook of RNA Biochemistry: Second, Completely Revised and Enlarged Edition / [ed] Roland K. Hartmann, Albrecht Bindereif, Astrid Schön, Eric Westhof, Weinheim: Wiley-Blackwell, 2014, 2, Vol. 1-2, p. 1-28Chapter in book (Other academic)
Place, publisher, year, edition, pages
Weinheim: Wiley-Blackwell, 2014 Edition: 2
Keywords
Double-stranded template, in vitro transcription, Modified nucleotide substrates, RNA with homogeneous and ends, Single-stranded template, T7 RNA polymerase, T7 RNA polymerase preparation
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-307114 (URN)10.1002/9783527647064.ch1 (DOI)2-s2.0-84977639757 (Scopus ID)9783527647064 (ISBN)9783527327645 (ISBN)
Available from: 2016-11-18 Created: 2016-11-08 Last updated: 2017-01-04Bibliographically approved
Kirsebom, L. A. & Ciesiolka, J. (2014). Pb2+-Induced Cleavage of RNA (2ed.). In: Roland K. Hartmann, Albrecht Bindereif, Astrid Schön, Eric Westhof (Ed.), Handbook of RNA Biochemistry: Second, Completely Revised and Enlarged Edition (pp. 269-284). Wiley-Blackwell, 1-2
Open this publication in new window or tab >>Pb2+-Induced Cleavage of RNA
2014 (English)In: Handbook of RNA Biochemistry: Second, Completely Revised and Enlarged Edition / [ed] Roland K. Hartmann, Albrecht Bindereif, Astrid Schön, Eric Westhof, Wiley-Blackwell, 2014, 2, Vol. 1-2, p. 269-284Chapter in book (Refereed)
Place, publisher, year, edition, pages
Wiley-Blackwell, 2014 Edition: 2
Keywords
In vitro and in vivo structural probing of RNA, Induced cleavage of RNA, Probing of metal ion binding sites in RNA, RNA-ligand interactions, Yeast tRNAPhe
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-307113 (URN)10.1002/9783527647064.ch13 (DOI)2-s2.0-84977619832 (Scopus ID)9783527647064 (ISBN)9783527327645 (ISBN)
Available from: 2016-11-21 Created: 2016-11-08 Last updated: 2017-01-04Bibliographically approved
Wu, S., Chen, Y., Mao, G., Trobro, S., Kwiatkowski, M. & Kirsebom, L. A. (2014). Transition-state stabilization in Escherichia coli ribonuclease P RNA-mediated cleavage of model substrates. Nucleic Acids Research, 42(1), 631-642
Open this publication in new window or tab >>Transition-state stabilization in Escherichia coli ribonuclease P RNA-mediated cleavage of model substrates
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2014 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 42, no 1, p. 631-642Article in journal (Refereed) Published
Abstract [en]

We have used model substrates carrying modified nucleotides at the site immediately 5' of the canonical RNase P cleavage site, the -1 position, to study Escherichia coli RNase P RNA-mediated cleavage. We show that the nucleobase at -1 is not essential but its presence and identity contribute to efficiency, fidelity of cleavage and stabilization of the transition state. When U or C is present at -1, the carbonyl oxygen at C2 on the nucleobase contributes to transition-state stabilization, and thus acts as a positive determinant. For substrates with purines at -1, an exocyclic amine at C2 on the nucleobase promotes cleavage at an alternative site and it has a negative impact on cleavage at the canonical site. We also provide new insights into the interaction between E. coli RNase P RNA and the -1 residue in the substrate. Our findings will be discussed using a model where bacterial RNase P cleavage proceeds through a conformational-assisted mechanism that positions the metal(II)-activated H2O for an in-line attack on the phosphorous atom that leads to breakage of the phosphodiester bond.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-221063 (URN)10.1093/nar/gkt853 (DOI)000331136000056 ()
Available from: 2014-03-26 Created: 2014-03-25 Last updated: 2017-12-05Bibliographically approved
Singh, B., Nitharwal, R. G., Ramesh, M., Pettersson, B. M., Kirsebom, L. A. & Dasgupta, S. (2013). Asymmetric growth and division in Mycobacterium spp.: compensatory mechanisms for non-medial septa. Molecular Microbiology, 88(1), 64-76
Open this publication in new window or tab >>Asymmetric growth and division in Mycobacterium spp.: compensatory mechanisms for non-medial septa
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2013 (English)In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 88, no 1, p. 64-76Article in journal (Refereed) Published
Abstract [en]

Mycobacterium spp., rod-shaped cells belonging to the phylum Actinomycetes, lack the Min- and Noc/Slm systems responsible for preventing the placement of division sites at the poles or over the nucleoids to ensure septal assembly at mid-cell. We show that the position for establishment of the FtsZ-ring in exponentially growing Mycobacterium marinum and Mycobacterium smegmatis cells is nearly random, and that the cells often divide non-medially, producing two unequal but viable daughters. Septal sites and cellular growth disclosed by staining with the membrane-specific dye FM4-64 and fluorescent antibiotic vancomycin (FL-Vanco), respectively, showed that many division sites were off-centre, often over the nucleoids, and that apical cell growth was frequently unequal at the two poles. DNA transfer through the division septum was detected, and translocation activity was supported by the presence of a putative mycobacterial DNA translocase (MSMEG2690) at the majority of the division sites. Time-lapse imaging of single live cells through several generations confirmed both acentric division site placement and unequal polar growth in mycobacteria. Our evidence suggests that post-septal DNA transport and unequal polar growth may compensate for the non-medial division site placement in Mycobacterium spp.

National Category
Medical and Health Sciences Natural Sciences
Identifiers
urn:nbn:se:uu:diva-199459 (URN)10.1111/mmi.12169 (DOI)000316812100006 ()
Available from: 2013-05-08 Created: 2013-05-06 Last updated: 2017-12-15
Pettersson, B. M., Nitharwal, R. G., Das, S., Behra, K. P. R., Benedik, E., Arasu, U. T., . . . Kirsebom, L. A. (2013). Identification and expression of stressosomal proteins in Mycobacterium marinum under various growth and stress conditions. FEMS Microbiology Letters, 342(2), 98-105
Open this publication in new window or tab >>Identification and expression of stressosomal proteins in Mycobacterium marinum under various growth and stress conditions
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2013 (English)In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 342, no 2, p. 98-105Article in journal (Refereed) Published
Abstract [en]

Like other bacteria, Mycobacterium spp. have developed different strategies in response to environmental changes such as nutrient limitations and other different stress situations. We have identified candidate genes (rsb genes) from Mycobacterium marinum involved in the regulation of the activity of the alternative sigma factor, sigma F. This is a homolog of the master regulator of general stress response, sigma B, and the sporulation-specific sigma factor, sigma F, in Bacillus subtilis. The organization of these genes in M.marinum and B.subtilis is similar. Transcriptome and qRT-PCR data show that these genes are indeed expressed in M.marinum and that the levels of expression vary with growth phase and exposure to stress. In particular, cold stress caused a significant rise in the expression of all identified rsb and sigF genes. We discuss these data in relation to what is currently known for other Mycobacterium spp.

Keywords
Mycobacterium marinum, transcriptome analysis, stress proteins
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-200667 (URN)10.1111/1574-6968.12118 (DOI)000318171000004 ()
Available from: 2013-06-03 Created: 2013-06-03 Last updated: 2017-12-06Bibliographically approved
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