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Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea.

Guo L, Feng Y, Zhang Z, Yao H, Luo Y, Wang J, Huang L - Nucleic Acids Res. (2007)

Bottom Line: A small, basic, methylated and abundant protein, Cren7 displays a higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils and is associated with genomic DNA in vivo.It interacts with duplex DNA through a beta-sheet and a long flexible loop, presumably resulting in DNA distortions through intercalation of conserved hydrophobic residues into the DNA structure.These data suggest that the crenarchaeal kingdom in the Archaea shares a common strategy in chromatin organization.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, PR China.

ABSTRACT
Archaea contain a variety of chromatin proteins consistent with the evolution of different genome packaging mechanisms. Among the two main kingdoms in the Archaea, Euryarchaeota synthesize histone homologs, whereas Crenarchaeota have not been shown to possess a chromatin protein conserved at the kingdom level. We report the identification of Cren7, a novel family of chromatin proteins highly conserved in the Crenarchaeota. A small, basic, methylated and abundant protein, Cren7 displays a higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils and is associated with genomic DNA in vivo. The solution structure and DNA-binding surface of Cren7 from the hyperthermophilic crenarchaeon Sulfolobus solfataricus were determined by NMR. The protein adopts an SH3-like fold. It interacts with duplex DNA through a beta-sheet and a long flexible loop, presumably resulting in DNA distortions through intercalation of conserved hydrophobic residues into the DNA structure. These data suggest that the crenarchaeal kingdom in the Archaea shares a common strategy in chromatin organization.

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Identification of the Cren7 protein family in Crenarchaea. (A) Purification of the S. shibatae Cren7 protein. Lane 1, cell lysate; lane 2, ammonium sulfate fraction; lane 3, SP Sepharose peak fractions; lane 4, Resource S peak fractions; lane 5, heparin peak fractions; lane 6, flow-through fractions from anti-Ssh7 antibody affinity column; lane 7, recombinant SsoCren7; lane 8, native Ssh10b; lane 9, native Ssh7; M, molecular weight standards with molecular weights indicated. (B) Sequence alignment of Cren7 homologs in Crenarchaea. Sequences are from Sulfolobus shibatae (SshCren7), Sulfolobus solfataricus P2 (SSO6901), Sulfolobus tokodaii str.7 (ST_3948), Sulfolobus acidocaldarius DSM 639 (Saci_1307), Metallosphaera sedula DSM5348 (Msed_1762), Aeropyrum pernix K1(APE_0450a), Staphylothermus marinus F1 (Smar_0237), Hyperthermus butylicus DSM5456 (Hbut_0878 and Hbut_1128), Ignicoccus hospitalis KIN4/I(Igni_0039), Pyrobaculum islandicum DSM4184 (Pisl_1589), Pyrobaculum aerophilum str. IM2 (PAE1516), Pyrobaculum arsenaticum DSM13514 (Pars_0631) and Pyrobaculum calidifontis JCM 11548 (Pcal_0878). (C) MALDI-TOF MS spectrum of native Cren7 from S. shibatae. A cluster of peaks with a mass difference of 14 kDa between adjacent peaks are shown.
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Figure 1: Identification of the Cren7 protein family in Crenarchaea. (A) Purification of the S. shibatae Cren7 protein. Lane 1, cell lysate; lane 2, ammonium sulfate fraction; lane 3, SP Sepharose peak fractions; lane 4, Resource S peak fractions; lane 5, heparin peak fractions; lane 6, flow-through fractions from anti-Ssh7 antibody affinity column; lane 7, recombinant SsoCren7; lane 8, native Ssh10b; lane 9, native Ssh7; M, molecular weight standards with molecular weights indicated. (B) Sequence alignment of Cren7 homologs in Crenarchaea. Sequences are from Sulfolobus shibatae (SshCren7), Sulfolobus solfataricus P2 (SSO6901), Sulfolobus tokodaii str.7 (ST_3948), Sulfolobus acidocaldarius DSM 639 (Saci_1307), Metallosphaera sedula DSM5348 (Msed_1762), Aeropyrum pernix K1(APE_0450a), Staphylothermus marinus F1 (Smar_0237), Hyperthermus butylicus DSM5456 (Hbut_0878 and Hbut_1128), Ignicoccus hospitalis KIN4/I(Igni_0039), Pyrobaculum islandicum DSM4184 (Pisl_1589), Pyrobaculum aerophilum str. IM2 (PAE1516), Pyrobaculum arsenaticum DSM13514 (Pars_0631) and Pyrobaculum calidifontis JCM 11548 (Pcal_0878). (C) MALDI-TOF MS spectrum of native Cren7 from S. shibatae. A cluster of peaks with a mass difference of 14 kDa between adjacent peaks are shown.

Mentions: In the process of purifying Ssh7, a member of the Sul7d family from S. shibatae, we co-purified a small, abundant protein (Figure 1A). LC-MS analysis identified this protein as a homolog of the product of an unknown gene (SSO6901) in the S. solfataricus P2 genome. Sequence comparison shows that this novel protein is highly conserved among the crenarchaeotal lineage of the Archaea (Figure 1B). All genome-sequenced Crenarchaea except for Thermofilum pendens Hrk5 and Cenarchaeum symbiosum encode a homolog of this protein. It is present in the orders Sulfolobales, Thermoproteales and Desulfurococcales. Since it was later shown to be a chromatin protein, we designate this novel protein family as Cren7 following the nomenclature used for Sul7d.Figure 1.


Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea.

Guo L, Feng Y, Zhang Z, Yao H, Luo Y, Wang J, Huang L - Nucleic Acids Res. (2007)

Identification of the Cren7 protein family in Crenarchaea. (A) Purification of the S. shibatae Cren7 protein. Lane 1, cell lysate; lane 2, ammonium sulfate fraction; lane 3, SP Sepharose peak fractions; lane 4, Resource S peak fractions; lane 5, heparin peak fractions; lane 6, flow-through fractions from anti-Ssh7 antibody affinity column; lane 7, recombinant SsoCren7; lane 8, native Ssh10b; lane 9, native Ssh7; M, molecular weight standards with molecular weights indicated. (B) Sequence alignment of Cren7 homologs in Crenarchaea. Sequences are from Sulfolobus shibatae (SshCren7), Sulfolobus solfataricus P2 (SSO6901), Sulfolobus tokodaii str.7 (ST_3948), Sulfolobus acidocaldarius DSM 639 (Saci_1307), Metallosphaera sedula DSM5348 (Msed_1762), Aeropyrum pernix K1(APE_0450a), Staphylothermus marinus F1 (Smar_0237), Hyperthermus butylicus DSM5456 (Hbut_0878 and Hbut_1128), Ignicoccus hospitalis KIN4/I(Igni_0039), Pyrobaculum islandicum DSM4184 (Pisl_1589), Pyrobaculum aerophilum str. IM2 (PAE1516), Pyrobaculum arsenaticum DSM13514 (Pars_0631) and Pyrobaculum calidifontis JCM 11548 (Pcal_0878). (C) MALDI-TOF MS spectrum of native Cren7 from S. shibatae. A cluster of peaks with a mass difference of 14 kDa between adjacent peaks are shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC2275093&req=5

Figure 1: Identification of the Cren7 protein family in Crenarchaea. (A) Purification of the S. shibatae Cren7 protein. Lane 1, cell lysate; lane 2, ammonium sulfate fraction; lane 3, SP Sepharose peak fractions; lane 4, Resource S peak fractions; lane 5, heparin peak fractions; lane 6, flow-through fractions from anti-Ssh7 antibody affinity column; lane 7, recombinant SsoCren7; lane 8, native Ssh10b; lane 9, native Ssh7; M, molecular weight standards with molecular weights indicated. (B) Sequence alignment of Cren7 homologs in Crenarchaea. Sequences are from Sulfolobus shibatae (SshCren7), Sulfolobus solfataricus P2 (SSO6901), Sulfolobus tokodaii str.7 (ST_3948), Sulfolobus acidocaldarius DSM 639 (Saci_1307), Metallosphaera sedula DSM5348 (Msed_1762), Aeropyrum pernix K1(APE_0450a), Staphylothermus marinus F1 (Smar_0237), Hyperthermus butylicus DSM5456 (Hbut_0878 and Hbut_1128), Ignicoccus hospitalis KIN4/I(Igni_0039), Pyrobaculum islandicum DSM4184 (Pisl_1589), Pyrobaculum aerophilum str. IM2 (PAE1516), Pyrobaculum arsenaticum DSM13514 (Pars_0631) and Pyrobaculum calidifontis JCM 11548 (Pcal_0878). (C) MALDI-TOF MS spectrum of native Cren7 from S. shibatae. A cluster of peaks with a mass difference of 14 kDa between adjacent peaks are shown.
Mentions: In the process of purifying Ssh7, a member of the Sul7d family from S. shibatae, we co-purified a small, abundant protein (Figure 1A). LC-MS analysis identified this protein as a homolog of the product of an unknown gene (SSO6901) in the S. solfataricus P2 genome. Sequence comparison shows that this novel protein is highly conserved among the crenarchaeotal lineage of the Archaea (Figure 1B). All genome-sequenced Crenarchaea except for Thermofilum pendens Hrk5 and Cenarchaeum symbiosum encode a homolog of this protein. It is present in the orders Sulfolobales, Thermoproteales and Desulfurococcales. Since it was later shown to be a chromatin protein, we designate this novel protein family as Cren7 following the nomenclature used for Sul7d.Figure 1.

Bottom Line: A small, basic, methylated and abundant protein, Cren7 displays a higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils and is associated with genomic DNA in vivo.It interacts with duplex DNA through a beta-sheet and a long flexible loop, presumably resulting in DNA distortions through intercalation of conserved hydrophobic residues into the DNA structure.These data suggest that the crenarchaeal kingdom in the Archaea shares a common strategy in chromatin organization.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, PR China.

ABSTRACT
Archaea contain a variety of chromatin proteins consistent with the evolution of different genome packaging mechanisms. Among the two main kingdoms in the Archaea, Euryarchaeota synthesize histone homologs, whereas Crenarchaeota have not been shown to possess a chromatin protein conserved at the kingdom level. We report the identification of Cren7, a novel family of chromatin proteins highly conserved in the Crenarchaeota. A small, basic, methylated and abundant protein, Cren7 displays a higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils and is associated with genomic DNA in vivo. The solution structure and DNA-binding surface of Cren7 from the hyperthermophilic crenarchaeon Sulfolobus solfataricus were determined by NMR. The protein adopts an SH3-like fold. It interacts with duplex DNA through a beta-sheet and a long flexible loop, presumably resulting in DNA distortions through intercalation of conserved hydrophobic residues into the DNA structure. These data suggest that the crenarchaeal kingdom in the Archaea shares a common strategy in chromatin organization.

Show MeSH
Related in: MedlinePlus