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Carlson, Karin
Alternative names
Publications (10 of 19) Show all publications
Carlson, K. & Linder, C. (2012). Introduktion till mikrobiologi: med inriktning mot naturvetare och farmaceuter, 2:a upplagan (2ed.). Lund: Studentlitteratur
Open this publication in new window or tab >>Introduktion till mikrobiologi: med inriktning mot naturvetare och farmaceuter, 2:a upplagan
2012 (Swedish)Book (Other academic)
Place, publisher, year, edition, pages
Lund: Studentlitteratur, 2012. p. 304 Edition: 2
National Category
Medical and Health Sciences
Research subject
Biology with specialization in Microbiology
Identifiers
urn:nbn:se:uu:diva-210906 (URN)978-91-44-07571-6 (ISBN)
Available from: 2013-11-15 Created: 2013-11-15 Last updated: 2013-11-15
Andersson, E., Lagerbäck, P. & Carlson, K. (2010). Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme. Journal of Molecular Biology, 397(4), 1003-1016
Open this publication in new window or tab >>Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme
2010 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 397, no 4, p. 1003-1016Article in journal (Refereed) Published
Abstract [en]

Coliphage T4 endonuclease II (EndoII), encoded by gene denA, is a small (16Da, 136aa) enzyme belonging to the GIY-YIG family of endonucleases, which lacks a C-terminal domain corresponding to that providing most of the binding energy in the structurally characterized GIY-YIG endonucleases, I-TevI and UvrC. In vivo, it is involved in degradation of host DNA, permitting scavenging of host-derived nucleotides for phage DNA synthesis. EndoII primarily catalyzes single-stranded nicking of DNA; 5- to 10-fold less frequently double-stranded breaks are produced. The Glu118Ala mutant of EndoII was crystallized in space group P21 with four monomers in the asymmetric unit. The fold of the EndoII monomer is similar to that of the catalytic domains of UvrC and I-TevI. In contrast to these enzymes, EndoII forms a striking X-shaped tetrameric structure composed as a dimer of dimers, with a protruding hairpin domain not present in UvrC or I-TevI providing most of the dimerization and tetramerization interfaces. A bound phosphate ion in one of the four active sites of EndoII likely mimics the scissile phosphate in a true substrate complex. In silico docking experiments showed that a protruding loop containing a nuclease-associated modular domain 3 element is likely to be involved in substrate binding, as well as residues forming a separate nucleic acid binding surface adjacent to the active site. The positioning of these sites within the EndoII primary dimer suggests that the substrate would bind to a primary EndoII dimer diagonally over the active sites, requiring significant distortion of the enzyme or the substrate DNA, or both, for simultaneous nicking of both DNA strands. The scarcity of potential nucleic acid binding residues between the active sites indicates that EndoII may bind its substrate inefficiently across the two sites in the dimer, offering a plausible explanation for the catalytic preponderance of single-strand nicks. Mutations analyzed in earlier functional studies are discussed in their structural context.

Keyword
Endonuclease, GIY-YIG, Phage, Tetramer, X-ray crystallography
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-97873 (URN)10.1016/j.jmb.2010.01.076 (DOI)000276566900013 ()20156453 (PubMedID)
Available from: 2008-11-27 Created: 2008-11-27 Last updated: 2017-12-14Bibliographically approved
Lagerbäck, P., Andersson, E., Malmberg, C. & Carlson, K. (2009). Bacteriophage T4 endonuclease II, a promiscuous GIY-YIG nuclease, binds as a tetramer to two DNA substrates. Nucleic Acids Research, 37(18), 6174-6183
Open this publication in new window or tab >>Bacteriophage T4 endonuclease II, a promiscuous GIY-YIG nuclease, binds as a tetramer to two DNA substrates
2009 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 37, no 18, p. 6174-6183Article in journal (Refereed) Published
Abstract [en]

The oligomerization state and mode of binding to DNA of the GIY-YIG   endonuclease II (EndoII) from bacteriophage T4 was studied using gel   filtration and electrophoretic mobility shift assays with a set of   mutants previously found to have altered enzyme activity. At low   enzyme/DNA ratios all mutants except one bound to DNA only as tetramers   to two DNA substrates. The putatively catalytic E118 residue actually   interfered with DNA binding (possibly due to steric hindrance or   repulsion between the glutamate side chain and DNA), as shown by the   ability of E118A to bind stably also as monomer or dimer to a single   substrate. The tetrameric structure of EndoII in the DNA-protein   complex is surprising considering the asymmetry of the recognized   sequence and the predominantly single-stranded nicking. Combining the   results obtained here with those from our previous in vivo studies and   the recently obtained crystal structure of EndoII E118A, we suggest a   model where EndoII translocates DNA between two adjacent binding sites   and either nicks one strand of one or both substrates bound by the   tetramer, or nicks both strands of one substrate. Thus, only one or two   of the four active sites in the tetramer is catalytically active at any time.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-97871 (URN)10.1093/nar/gkp652 (DOI)000271109300027 ()19666720 (PubMedID)
Available from: 2008-11-27 Created: 2008-11-27 Last updated: 2017-12-14Bibliographically approved
Lagerbäck, P. & Carlson, K. (2008). Amino acid residues in the GIY-YIG endonuclease II of phage T4 affecting sequence recognition and binding as well as catalysis. Journal of Bacteriology, 190(16), 5533-5544
Open this publication in new window or tab >>Amino acid residues in the GIY-YIG endonuclease II of phage T4 affecting sequence recognition and binding as well as catalysis
2008 (English)In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 190, no 16, p. 5533-5544Article in journal (Refereed) Published
Abstract [en]

Phage T4 endonuclease II (EndoII), a GIY-YIG endonuclease lackinga carboxy-terminal DNA-binding domain, was subjected to site-directedmutagenesis to investigate roles of individual amino acids insubstrate recognition, binding, and catalysis. The structureof EndoII was modeled on that of UvrC. We found catalytic rolesfor residues in the putative catalytic surface (G49, R57, E118,and N130) similar to those described for I-TevI and UvrC; inaddition, these residues were found to be important for substraterecognition and binding. The conserved glycine (G49) and arginine(R57) were essential for normal sequence recognition. Our resultsare in agreement with a role for these residues in forming theDNA-binding surface and exposing the substrate scissile bondat the active site. The conserved asparagine (N130) and an adjacentproline (P127) likely contribute to positioning the catalyticdomain correctly. Enzymes in the EndoII subfamily of GIY-YIGendonucleases share a strongly conserved middle region (MR,residues 72 to 93, likely helical and possibly substitutingfor heterologous helices in I-TevI and UvrC) and a less stronglyconserved N-terminal region (residues 12 to 24). Most of theconserved residues in these two regions appeared to contributeto binding strength without affecting the mode of substratebinding at the catalytic surface. EndoII K76, part of a conservedNUMOD3 DNA-binding motif of homing endonucleases found to overlapthe MR, affected both sequence recognition and catalysis, suggestinga more direct involvement in positioning the substrate. Ourdata thus suggest roles for the MR and residues conserved inGIY-YIG enzymes in recognizing and binding the substrate.

Keyword
phage T4, GIY-YIG endonuclease, nicking, structure modeling, sequence recognition, information content
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-97870 (URN)10.1128/JB.00094-08 (DOI)000258274400001 ()
Available from: 2008-11-27 Created: 2008-11-27 Last updated: 2017-12-14Bibliographically approved
Carlson, K. & Linder, C. (2008). Introduktion till mikrobiologi: med inriktning mot naturvetare och farmaceuter. (1ed.). Studentlitteratur
Open this publication in new window or tab >>Introduktion till mikrobiologi: med inriktning mot naturvetare och farmaceuter.
2008 (Swedish)Book (Other academic)
Place, publisher, year, edition, pages
Studentlitteratur, 2008. p. 239 Edition: 1
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-12866 (URN)9789144048468 (ISBN)
Available from: 2008-01-18 Created: 2008-01-18 Last updated: 2018-01-12Bibliographically approved
Carlson, K. & Halldin, S. (2006). Naturvetarsvenskan förtvinar. Språkvård (2006/2), 36-38
Open this publication in new window or tab >>Naturvetarsvenskan förtvinar
2006 (Swedish)In: Språkvård, no 2006/2, p. 36-38Article in journal (Other (popular scientific, debate etc.)) Published
Abstract [en]

Engelska för forskningen, svenskan för forskningsinformationen och båda språken i utbildningen. Ungefär så ville Kerstin Norén, prorektor vid Göteborgs universitet, ordna högskolans språkval i en artikel i Språkvård 2006/1. Karin Carlson och Sven Halldin, båda verksamma i Uppsala uiversitets naturvetenskapliga språkgrupp, tycker att det inte är så enkelt.

Keyword
naturvetare, språk, terminologi, domänförluster
National Category
Communication Studies
Identifiers
urn:nbn:se:uu:diva-21851 (URN)
Note
Karin Carlson är biträdande professor i mikrobiologi vid Uppsala universitet och även ledamot i teknisk-naturvetenskapliga fakultetens språkgrupp och biotermgruppen. Hon medverkade senast i Språkvård 2002:2 med artikeln ”Tvåspråkiga naturvetare”.Available from: 2007-01-05 Created: 2007-01-05 Last updated: 2011-01-11
Halldin, S. & Carlson, K. (2006). Svenska språket är hotat inom naturvetenskapen. Tentakel, 9
Open this publication in new window or tab >>Svenska språket är hotat inom naturvetenskapen
2006 (Swedish)In: Tentakel, Vol. 9Article in journal (Other (popular scientific, debate etc.)) Published
Abstract [en]

Svensk naturvetenskap och teknik är på väg att förlora modersmålet. Det storskaliga språkbytet leder till försämrad effektivitet och ett demokratiskt underskott. Medvetenheten om problemen måste öka och en fungerande tvåspråkighet etableras.

Keyword
naturvetare, språk, terminologi, domänförluster
National Category
Communication Studies
Identifiers
urn:nbn:se:uu:diva-21852 (URN)
Available from: 2007-01-05 Created: 2007-01-05 Last updated: 2011-01-11
Carlson, K., Kiselman, C., Danielsson, U., Halldin, S. & Mattsson, A. (2005). Language policy for a bilingual faculty. In: Bi- and multilingual universities, Helsinki, Finland, Sept 1-3, 2005.
Open this publication in new window or tab >>Language policy for a bilingual faculty
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2005 (English)In: Bi- and multilingual universities, Helsinki, Finland, Sept 1-3, 2005, 2005Conference paper, Published paper (Refereed)
Abstract [en]

The Faculty of Science and Technology of Uppsala University is for all practical purposes a bilingual institution, using both Swedish and English in education and research. Extensive use of English in teaching, and also in intrauniversity communication, permits recruitment of nonSwedishspeaking students, researchers and professors, and also prepares our students for

international careers. However, the introduction of English has been somewhat haphazard, not taking into account possible negative effects on communication in Swedish, nor on students'

learning.

In order to improve students' and professors' language skills, and achieve a good balance between Swedish and English, the faculty board appointed a language committee in 2003 whose task was to propose a language policy for the faculty. A first part, stating as a main goal that all communication from and within the faculty should have the highest quality possible, has been adopted by the board. A second part including language planning with respect to status, corpus, and acquisition for both Swedish and English to accomplish this goal was sent to the board of the faculty in May, 2005. Implementation of this policy will affect all faculty activities, especially education. Suggested

annual reports on language status will raise our present minimal knowledge about possible domain losses and allow for relevant countermeasures.

Identifiers
urn:nbn:se:uu:diva-77658 (URN)
Available from: 2006-03-15 Created: 2006-03-15
Kutter, E., Raya, R. & Carlson, K. (2005). Molecular mechanisms of phage infection. In: Bacteriophages: Molecular Biology and Applications.
Open this publication in new window or tab >>Molecular mechanisms of phage infection
2005 (English)In: Bacteriophages: Molecular Biology and Applications, 2005Chapter in book (Other (popular scientific, debate etc.))
Abstract [en]

Synthetic sites inserted into a plasmid were used to analyze the sequence requirements for in vivo DNA cleavage dependent on bacteriophage T4 endonuclease II. A 16-bp variable sequence surrounding the cleavage site was sufficient for cleavage, although context both within and around this sequence influenced cleavage efficiency. The most efficiently cleaved sites matched the sequence CGRCCGCNTTGGCNGC, in which the strongly conserved bases to the left were essential for cleavage. The less-conserved bases in the center and in the right half determined cleavage efficiency in a manner not directly correlated with the apparent base preference at each position; a sequence carrying, in each of the 16 positions, the base most preferred in natural sites in pBR322 was cleaved infrequently. This, along with the effects of substitutions at one or two of the less-conserved positions, suggests that several combinations of bases can fulfill the requirements for recognition of the right part of this sequence. The replacements that improve cleavage frequency are predicted to influence helical twist and roll, suggesting that recognition of sequence-dependent DNA structure and recognition of specific bases are both important. Upon introduction of a synthetic site, cleavage at natural sites within 800 to 1,500 bp from the synthetic site was significantly reduced. This suggests that the enzyme may engage more DNA than its cleavage site and cleaves the best site within this region. Cleavage frequency at sites which do not conform closely to the consensus is, therefore, highly context dependent. Models and possible biological implications of these findings are discussed.

Keyword
naturvetare, språk, terminologi, domänförluster
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-75939 (URN)
Note
Publicerad i Kemivärlden Biotech nr. 11-12, 2004Available from: 2006-02-23 Created: 2006-02-23
Kiselman, C., Halldin, S., Danielsson, U., Carlson, K., Mattsson, A. & Rutberg, M. (2005). "Svenska språket dör ut på landets universitet": DN - Debatt. Dagens Nyheter (2005-06-17)
Open this publication in new window or tab >>"Svenska språket dör ut på landets universitet": DN - Debatt
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2005 (Swedish)In: Dagens Nyheter, no 2005-06-17Article in journal (Other (popular scientific, debate etc.)) Published
Keyword
Språkpolitik
National Category
Mathematics Oceanography, Hydrology and Water Resources Physical Sciences Biological Sciences
Identifiers
urn:nbn:se:uu:diva-77712 (URN)
Available from: 2007-01-23 Created: 2007-01-23 Last updated: 2018-01-13
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