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Johansson, Erik
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Publications (10 of 48) Show all publications
Rentoft, M., Svensson, D., Sjödin, A., Olason, P. I., Sjöström, O., Nylander, C., . . . Johansson, E. (2019). A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis. PLoS ONE, 14(3), Article ID e0213350.
Open this publication in new window or tab >>A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis
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2019 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 14, no 3, article id e0213350Article in journal (Refereed) Published
Abstract [en]

Whole-genome sequencing is a promising approach for human autosomal dominant disease studies. However, the vast number of genetic variants observed by this method constitutes a challenge when trying to identify the causal variants. This is often handled by restricting disease studies to the most damaging variants, e.g. those found in coding regions, and overlooking the remaining genetic variation. Such a biased approach explains in part why the genetic causes of many families with dominantly inherited diseases, in spite of being included in whole-genome sequencing studies, are left unsolved today. Here we explore the use of a geographically matched control population to minimize the number of candidate disease-causing variants without excluding variants based on assumptions on genomic position or functional predictions. To exemplify the benefit of the geographically matched control population we apply a typical disease variant filtering strategy in a family with an autosomal dominant form of colorectal cancer. With the use of the geographically matched control population we end up with 26 candidate variants genome wide. This is in contrast to the tens of thousands of candidates left when only making use of available public variant datasets. The effect of the local control population is dual, it (1) reduces the total number of candidate variants shared between affected individuals, and more importantly (2) increases the rate by which the number of candidate variants are reduced as additional affected family members are included in the filtering strategy. We demonstrate that the application of a geographically matched control population effectively limits the number of candidate disease-causing variants and may provide the means by which variants suitable for functional studies are identified genome wide.

Place, publisher, year, edition, pages
Public Library of Science, 2019
National Category
Medical Genetics
Identifiers
urn:nbn:se:umu:diva-158021 (URN)10.1371/journal.pone.0213350 (DOI)000462465800028 ()30917156 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation, 2011.0042
Available from: 2019-04-10 Created: 2019-04-10 Last updated: 2019-04-12Bibliographically approved
Parkash, V., Kulkarni, Y., ter Beek, J., Shcherbakova, P. V., Kamerlin, S. C. & Johansson, E. (2019). Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon. Nature Communications, 10, Article ID 373.
Open this publication in new window or tab >>Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon
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2019 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 373Article in journal (Refereed) Published
Abstract [en]

The most frequently recurring cancer-associated DNA polymerase epsilon (Pol epsilon) mutation is a P286R substitution in the exonuclease domain. While originally proposed to increase genome instability by disrupting exonucleolytic proofreading, the P286R variant was later found to be significantly more pathogenic than Pol epsilon proofreading deficiency per se. The mechanisms underlying its stronger impact remained unclear. Here we report the crystal structure of the yeast orthologue, Pol epsilon-P301R, complexed with DNA and an incoming dNTP. Structural changes in the protein are confined to the exonuclease domain, with R301 pointing towards the exonuclease site. Molecular dynamics simulations suggest that R301 interferes with DNA binding to the exonuclease site, an outcome not observed with the exonuclease-inactive Pol epsilon-D290A, E292A variant lacking the catalytic residues. These results reveal a distinct mechanism of exonuclease inactivation by the P301R substitution and a likely basis for its dramatically higher mutagenic and tumorigenic effects.

Place, publisher, year, edition, pages
Nature Publishing Group, 2019
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-156315 (URN)10.1038/s41467-018-08114-9 (DOI)000456286400001 ()30670696 (PubMedID)
Available from: 2019-02-21 Created: 2019-02-21 Last updated: 2019-02-21Bibliographically approved
ter Beek, J., Parkash, V., Bylund, G., Osterman, P., Sauer-Eriksson, A. E. & Johansson, E. (2019). Structural evidence for an essential Fe–S cluster in the catalytic core domain of DNA polymerase ϵ. Nucleic Acids Research, 47(11), 5712-5722
Open this publication in new window or tab >>Structural evidence for an essential Fe–S cluster in the catalytic core domain of DNA polymerase ϵ
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2019 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 47, no 11, p. 5712-5722Article in journal (Refereed) Published
Abstract [en]

DNA polymerase ϵ (Pol ϵ), the major leading-strand DNA polymerase in eukaryotes, has a catalytic subunit (Pol2) and three non-catalytic subunits. The N-terminal half of Pol2 (Pol2CORE) exhibits both polymerase and exonuclease activity. It has been suggested that both the non-catalytic C-terminal domain of Pol2 (with the two cysteine motifs CysA and CysB) and Pol2CORE (with the CysX cysteine motif) are likely to coordinate an Fe–S cluster. Here, we present two new crystal structures of Pol2CORE with an Fe–S cluster bound to the CysX motif, supported by an anomalous signal at that position. Furthermore we show that purified four-subunit Pol ϵ, Pol ϵ CysAMUT (C2111S/C2133S), and Pol ϵ CysBMUT (C2167S/C2181S) all have an Fe–S cluster that is not present in Pol ϵ CysXMUT (C665S/C668S). Pol ϵ CysAMUT and Pol ϵ CysBMUT behave similarly to wild-type Pol ϵ in in vitro assays, but Pol ϵ CysXMUT has severely compromised DNA polymerase activity that is not the result of an excessive exonuclease activity. Tetrad analyses show that haploid yeast strains carrying CysXMUT are inviable. In conclusion, Pol ϵ has a single Fe–S cluster bound at the base of the P-domain, and this Fe–S cluster is essential for cell viability and polymerase activity.

Place, publisher, year, edition, pages
Oxford University Press, 2019
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-161925 (URN)10.1093/nar/gkz248 (DOI)000475702000027 ()30968138 (PubMedID)2-s2.0-85068487970 (Scopus ID)
Available from: 2019-08-06 Created: 2019-08-06 Last updated: 2019-08-06Bibliographically approved
Yu, C., Gan, H., Serra-Cardona, A., Zhang, L., Gan, S., Sharma, S., . . . Zhang, Z. (2018). A mechanism for preventing asymmetric histone segregation onto replicating DNA strands. Science, 361(6409), 1386-+, Article ID eaat8849.
Open this publication in new window or tab >>A mechanism for preventing asymmetric histone segregation onto replicating DNA strands
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2018 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 361, no 6409, p. 1386-+-, article id eaat8849Article in journal (Refereed) Published
Abstract [en]

How parental histone (H3-H4)2 tetramers, the primary carriers of epigenetic modifications, are transferred onto leading and lagging strands of DNA replication forks for epigenetic inheritance remains elusive. Here we show that parental (H3-H4)2 tetramers are assembled into nucleosomes onto both leading and lagging strands, with a slight preference for lagging strands. The lagging strand preference increases markedly in cells lacking Dpb3 and Dpb4, two subunits of the leading strand DNA polymerase, Pol ε, due to the impairment of parental (H3-H4)2 transfer to leading strands. Dpb3-Dpb4 binds H3-H4 in vitro and participates in the inheritance of heterochromatin. These results indicate that different proteins facilitate the transfer of parental (H3-H4)2 onto leading vs lagging strands, and that Dbp3-Dpb4 plays a significant role in this poorly understood process.

Place, publisher, year, edition, pages
American Association for the Advancement of Science, 2018
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-150963 (URN)10.1126/science.aat8849 (DOI)000446142200050 ()30115745 (PubMedID)
Funder
NIH (National Institute of Health), R35GM118015Swedish Cancer SocietySwedish Research Council
Note

Special Issue: SI

Available from: 2018-08-21 Created: 2018-08-21 Last updated: 2018-10-31Bibliographically approved
Ganai, R. A. & Johansson, E. (2016). DNA Replication - A Matter of Fidelity. Molecular Cell, 62(5), 745-755
Open this publication in new window or tab >>DNA Replication - A Matter of Fidelity
2016 (English)In: Molecular Cell, ISSN 1097-2765, E-ISSN 1097-4164, Vol. 62, no 5, p. 745-755Article, review/survey (Refereed) Published
Abstract [en]

The fidelity of DNA replication is determined by many factors, here simplified as the contribution of the DNA polymerase (nucleotide selectivity and proofreading), mismatch repair, a balanced supply of nucleotides, and the condition of the DNA template (both in terms of sequence context and the presence of DNA lesions). This review discusses the contribution and interplay between these factors to the overall fidelity of DNA replication.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-122545 (URN)10.1016/j.molcel.2016.05.003 (DOI)000377049500011 ()27259205 (PubMedID)
Available from: 2016-07-26 Created: 2016-06-20 Last updated: 2018-06-07Bibliographically approved
Rentoft, M., Lindell, K., Tran, P., Chabes, A. L., Buckland, R., Watt, D. L., . . . Chabes, A. (2016). Heterozygous colon cancer-associated mutations of SAMHD1 have functional significance. Proceedings of the National Academy of Sciences of the United States of America, 113(17), 4723-4728
Open this publication in new window or tab >>Heterozygous colon cancer-associated mutations of SAMHD1 have functional significance
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2016 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 17, p. 4723-4728Article in journal (Refereed) Published
Abstract [en]

Even small variations in dNTP concentrations decrease DNA replication fidelity, and this observation prompted us to analyze genomic cancer data for mutations in enzymes involved in dNTP metabolism. We found that sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1), a deoxyribonucleoside triphosphate triphosphohydrolase that decreases dNTP pools, is frequently mutated in colon cancers, that these mutations negatively affect SAMHD1 activity, and that severalSAMHD1mutations are found in tumors with defective mismatch repair. We show that minor changes in dNTP pools in combination with inactivated mismatch repair dramatically increase mutation rates. Determination of dNTP pools in mouse embryos revealed that inactivation of oneSAMHD1allele is sufficient to elevate dNTP pools. These observations suggest that heterozygous cancer-associatedSAMHD1mutations increase mutation rates in cancer cells.

National Category
Cell and Molecular Biology
Research subject
cell research
Identifiers
urn:nbn:se:umu:diva-119232 (URN)10.1073/pnas.1519128113 (DOI)000374748400052 ()27071091 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Cancer SocietySwedish Research Council
Available from: 2016-04-14 Created: 2016-04-14 Last updated: 2018-06-07Bibliographically approved
Ganai, R. A., Zhang, X.-P., Heyer, W.-D. & Johansson, E. (2016). Strand displacement synthesis by yeast DNA polymerase epsilon. Nucleic Acids Research, 44(17), 8229-8240
Open this publication in new window or tab >>Strand displacement synthesis by yeast DNA polymerase epsilon
2016 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 44, no 17, p. 8229-8240Article in journal (Refereed) Published
Abstract [en]

DNA polymerase epsilon (Pol epsilon) is a replicative DNA polymerase with an associated 3'aEuro"5' exonuclease activity. Here, we explored the capacity of Pol epsilon to perform strand displacement synthesis, a process that influences many DNA transactions in vivo. We found that Pol epsilon is unable to carry out extended strand displacement synthesis unless its 3'aEuro"5' exonuclease activity is removed. However, the wild-type Pol epsilon holoenzyme efficiently displaced one nucleotide when encountering double-stranded DNA after filling a gap or nicked DNA. A flap, mimicking a D-loop or a hairpin structure, on the 5' end of the blocking primer inhibited Pol epsilon from synthesizing DNA up to the fork junction. This inhibition was observed for Pol epsilon but not with Pol delta, RB69 gp43 or Pol eta. Neither was Pol epsilon able to extend a D-loop in reconstitution experiments. Finally, we show that the observed strand displacement synthesis by exonuclease-deficient Pol epsilon is distributive. Our results suggest that Pol epsilon is unable to extend the invading strand in D-loops during homologous recombination or to add more than two nucleotides during long-patch base excision repair. Our results support the hypothesis that Pol epsilon participates in short-patch base excision repair and ribonucleotide excision repair.

Place, publisher, year, edition, pages
Oxford University Press, 2016
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:umu:diva-130111 (URN)10.1093/nar/gkw556 (DOI)000386158800023 ()27325747 (PubMedID)
Available from: 2017-01-13 Created: 2017-01-11 Last updated: 2018-06-09Bibliographically approved
Yousefzadeh, M. J., Wyatt, D. W., Takata, K., Mu, Y., Hensley, S. C., Tomida, J., . . . Wood, R. D. (2015). Mammalian POLQ, Chromosome Stability and DNA Double-Strand Break Repair. Environmental and Molecular Mutagenesis, 56, S48-S48
Open this publication in new window or tab >>Mammalian POLQ, Chromosome Stability and DNA Double-Strand Break Repair
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2015 (English)In: Environmental and Molecular Mutagenesis, ISSN 0893-6692, E-ISSN 1098-2280, Vol. 56, p. S48-S48Article in journal, Meeting abstract (Other academic) Published
National Category
Pharmacology and Toxicology Medical Genetics
Identifiers
urn:nbn:se:umu:diva-108466 (URN)000360226400070 ()
Available from: 2015-09-14 Created: 2015-09-11 Last updated: 2018-06-07Bibliographically approved
Ganai, R. A., Bylund, G. & Johansson, E. (2015). Switching between polymerase and exonuclease sites in DNA polymerase ε. Nucleic Acids Research, 43(2), 932-942
Open this publication in new window or tab >>Switching between polymerase and exonuclease sites in DNA polymerase ε
2015 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 43, no 2, p. 932-942Article in journal (Refereed) Published
Abstract [en]

The balance between exonuclease and polymerase activities promotes DNA synthesis over degradation when nucleotides are correctly added to the new strand by replicative B-family polymerases. Misincorporations shift the balance toward the exonuclease site, and the balance tips back in favor of DNA synthesis when the incorrect nucleotides have been removed. Most B-family DNA polymerases have an extended β-hairpin loop that appears to be important for switching from the exonuclease site to the polymerase site, a process that affects fidelity of the DNA polymerase. Here, we show that DNA polymerase ε can switch between the polymerase site and exonuclease site in a processive manner despite the absence of an extended β-hairpin loop. K967 and R988 are two conserved amino acids in the palm and thumb domain that interact with bases on the primer strand in the minor groove at positions n−2 and n−4/n−5, respectively. DNA polymerase ε depends on both K967 and R988 to stabilize the 3′-terminus of the DNA within the polymerase site and on R988 to processively switch between the exonuclease and polymerase sites. Based on a structural alignment with DNA polymerase δ, we propose that arginines corresponding to R988 might have a similar function in other B-family polymerases.

Place, publisher, year, edition, pages
Oxford University Press, 2015
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-97693 (URN)10.1093/nar/gku1353 (DOI)000350209000027 ()25550436 (PubMedID)
Available from: 2015-01-08 Created: 2015-01-05 Last updated: 2018-06-07Bibliographically approved
Ganai, R. A., Osterman, P. & Johansson, E. (2015). Yeast DNA Polymerase epsilon Catalytic Core and Holoenzyme Have Comparable Catalytic Rates. Journal of Biological Chemistry, 290(6), 3825-3835
Open this publication in new window or tab >>Yeast DNA Polymerase epsilon Catalytic Core and Holoenzyme Have Comparable Catalytic Rates
2015 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 290, no 6, p. 3825-3835Article in journal (Refereed) Published
Abstract [en]

The holoenzyme of yeast DNApolymerase ε (Pol ε) consists of four subunits– Pol2, Dpb2, Dpb3, and Dpb4. A proteasesensitivesite results in a N-terminalproteolytic fragment of Pol2, called Pol2core,that consists of the catalytic core of Pol ε andretains both polymerase and exonucleaseactivities. Pre-steady-state kinetics showedthat the exonuclease rates on single-stranded,double-stranded, and mismatched DNA werecomparable between Pol ε and Pol2core. Singleturnover pre-steady-state kinetics alsoshowed that the kpol of Pol ε and Pol2core werecomparable when pre-loading the polymeraseonto the primer-template before adding Mg2+and dTTP. However, a global fit of the dataover six sequential nucleotide incorporationsrevealed that the overall polymerization rateand processivity was higher for Pol ε than forPol2core. The largest difference was observedwhen challenged for the formation of aternary complex and incorporation of thefirst nucleotide. Pol ε needed less than asecond to incorporate a nucleotide, butseveral seconds passed before Pol2coreincorporated detectable levels of the firstnucleotide. We conclude that the accessorysubunits and the C-terminus of Pol2 do notinfluence the catalytic rate of Pol ε butfacilitate the loading and incorporation of thefirst nucleotide by Pol ε.

Place, publisher, year, edition, pages
USA: , 2015
Keywords
DNA polymerase, DNA repair, DNA replication, enzyme catalysis, enzyme kinetics
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:umu:diva-97692 (URN)10.1074/jbc.M114.615278 (DOI)000349456000053 ()25538242 (PubMedID)
Available from: 2015-01-08 Created: 2015-01-05 Last updated: 2018-06-07Bibliographically approved
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