Two possible type I restriction-modification (R-M) systems, KpnAI and KpnBl, were recognized in Klebsiella pneumoniae strains M5al and GM236, respectively. In this project, four hsdRKpnAI clones (pNLA1 to pNLA4) were obtained by using an endonuclease expression-selection method. The hsdRKpnAI gene was identified on a 3.6 kb Sau3Al fragment. To map the gene, the hsdRKpnAI clone was hybridized to a membrane which contained pulsed-field gel electrophoresed fragments of the chromosome of the strain M5al. The hsdRKpnAI clone was hybridized to a 19 kb Xbal fragment and a 420 kb Blnl fragment, located at about 16 to 20 min on the recently constructed physical map of the M5al chromosome.
Similarly, the hsdRKpnBI clone was hybridized to a 40 kb Xbal fragment and a 330 kb Blnl fragment of the GM236 chromosome. Among five subclones (pNLB1 to pNLB5), the 3.5 kb BamHI-EcoRl fragment of pNLB2 was the smallest DNA fragment to retain restriction activity through complementation testing. The DNA sequence of the 3.5 kb fragment was determined. An open reading frame (ORF) of 3,039 bp was concluded to be the coding region for the HsdRkpnBI polypeptide. The 1,013 amino acid product (111,430 daltons) deduced from the nucleotide sequence is in excellent agreement with the 116 kD size estimated from the electrophoretic mobility of the putative HsdRkpnBI protein in SDS polyacrylamide gels. The nucleotide sequence of the hsdRkpnBI gene showed no significant similarity to any other sequence in the GenBank database. However, a homology search of the amino acid sequence scored highly with EcoR124/3I, a type IC restriction enzyme. After alignment of the two proteins, two ATP binding domains, a DNA binding domain and seven helicase motifs were found. Eight small ORFs were identified within a few kb on either side of the hsdRKpnBI gene. When subcloned, none of these ORFs showed any modification activity. However, complementation with r-KpnBI m-KpnBI mutant suggests that one downstream ORF is a positive effector for expression of the KpnBI modification activity.
","abstract_html":"<p>Two possible type I restriction-modification (R-M) systems, <em>Kpn</em>AI and <em>Kpn</em>Bl, were recognized in <em>Klebsiella pneumoniae</em> strains M5al and GM236, respectively. In this project, four <em>hsdR</em><sub>KpnAI</sub> clones (pNLA1 to pNLA4) were obtained by using an endonuclease expression-selection method. The <em>hsdR</em><sub>KpnAI</sub> gene was identified on a 3.6 kb <em>Sau3</em>Al fragment. To map the gene, the <em>hsdR</em><sub>KpnAI</sub> clone was hybridized to a membrane which contained pulsed-field gel electrophoresed fragments of the chromosome of the strain M5al. The <em>hsdR</em><sub>KpnAI </sub>clone was hybridized to a 19 kb <em>Xba</em>l fragment and a 420 kb <em>Bln</em>l fragment, located at about 16 to 20 min on the recently constructed physical map of the M5al chromosome.</p> <p>Similarly, the <em>hsdR</em><sub>KpnBI</sub> clone was hybridized to a 40 kb <em>Xba</em>l fragment and a 330 kb <em>Bln</em>l fragment of the GM236 chromosome. Among five subclones (pNLB1 to pNLB5), the 3.5 kb <em>Bam</em>HI-<em>Eco</em>Rl fragment of pNLB2 was the smallest DNA fragment to retain restriction activity through complementation testing. The DNA sequence of the 3.5 kb fragment was determined. An open reading frame (ORF) of 3,039 bp was concluded to be the coding region for the HsdR<sub>kpnBI </sub>polypeptide. The 1,013 amino acid product (111,430 daltons) deduced from the nucleotide sequence is in excellent agreement with the 116 kD size estimated from the electrophoretic mobility of the putative HsdR<sub>kpnBI </sub>protein in SDS polyacrylamide gels. The nucleotide sequence of the hsdR<sub>kpnBI </sub>gene showed no significant similarity to any other sequence in the GenBank database. However, a homology search of the amino acid sequence scored highly with <em>Eco</em>R124/3I, a type IC restriction enzyme. After alignment of the two proteins, two ATP binding domains, a DNA binding domain and seven helicase motifs were found. Eight small ORFs were identified within a few kb on either side of the <em>hsdR</em><sub>KpnBI</sub> gene. When subcloned, none of these ORFs showed any modification activity. However, complementation with r<sup>-</sup><sub>KpnBI</sub> m<sup>-</sup><sub>KpnBI </sub>mutant suggests that one downstream ORF is a positive effector for expression of the KpnBI modification activity.</p>","abstract_has_math":false,"creators":["Lee, Nan Sook"],"institution":null,"degree_name":"Doctor of Philosophy (Medical Science)","degree_level":"Dissertation","degree_discipline":"Microbiology","degree_department":null,"school":null,"contributors":["Junichi Ryu","Leonard R. Bullas","Kelvin A. W. Hill","John J. Rossi","Anthony J. Zuccarelli"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":1994,"date_issued":"1994-08-01T07:00:00Z","date_published":"1994-08-01T07:00:00Z","updated_at":"2026-07-24T02:53:44Z","subjects":["Microbiology","Klebsiella pneumoniae -- genetics; Restriction Mapping Cloning; Molecular"],"languages":["English"],"rights":["This title appears here courtesy of the author, who has granted Loma Linda University a limited, non-exclusive right to make this publication available to the public. The author retains all other copyrights."],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://scholarsrepository.llu.edu/etd/1404","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Junichi Ryu","Leonard R. Bullas","Kelvin A. W. Hill","John J. Rossi","Anthony J. Zuccarelli"]},{"key":"dc:creator","label":"Author","values":["Lee, Nan Sook"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"thesis:degree_discipline","label":"Discipline","values":["Microbiology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy (Medical Science)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Microbiology","Klebsiella pneumoniae -- genetics; Restriction Mapping Cloning; Molecular"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["English"]},{"key":"dc:rights","label":"Dc Rights","values":["This title appears here courtesy of the author, who has granted Loma Linda University a limited, non-exclusive right to make this publication available to the public. The author retains all other copyrights."]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://scholarsrepository.llu.edu/etd/1404"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Two possible type I restriction-modification (R-M) systems, KpnAI and KpnBl, were recognized in Klebsiella pneumoniae strains M5al and GM236, respectively. In this project, four hsdRKpnAI clones (pNLA1 to pNLA4) were obtained by using an endonuclease expression-selection method. The hsdRKpnAI gene was identified on a 3.6 kb Sau3Al fragment. To map the gene, the hsdRKpnAI clone was hybridized to a membrane which contained pulsed-field gel electrophoresed fragments of the chromosome of the strain M5al. The hsdRKpnAI clone was hybridized to a 19 kb Xbal fragment and a 420 kb Blnl fragment, located at about 16 to 20 min on the recently constructed physical map of the M5al chromosome.
Similarly, the hsdRKpnBI clone was hybridized to a 40 kb Xbal fragment and a 330 kb Blnl fragment of the GM236 chromosome. Among five subclones (pNLB1 to pNLB5), the 3.5 kb BamHI-EcoRl fragment of pNLB2 was the smallest DNA fragment to retain restriction activity through complementation testing. The DNA sequence of the 3.5 kb fragment was determined. An open reading frame (ORF) of 3,039 bp was concluded to be the coding region for the HsdRkpnBI polypeptide. The 1,013 amino acid product (111,430 daltons) deduced from the nucleotide sequence is in excellent agreement with the 116 kD size estimated from the electrophoretic mobility of the putative HsdRkpnBI protein in SDS polyacrylamide gels. The nucleotide sequence of the hsdRkpnBI gene showed no significant similarity to any other sequence in the GenBank database. However, a homology search of the amino acid sequence scored highly with EcoR124/3I, a type IC restriction enzyme. After alignment of the two proteins, two ATP binding domains, a DNA binding domain and seven helicase motifs were found. Eight small ORFs were identified within a few kb on either side of the hsdRKpnBI gene. When subcloned, none of these ORFs showed any modification activity. However, complementation with r-KpnBI m-KpnBI mutant suggests that one downstream ORF is a positive effector for expression of the KpnBI modification activity.
"]},{"key":"dc:title","label":"Title","values":["Molecular Studies of KpnAI and KpnBI R-M Systems : in KLEBSIELLA PNEUMONIAE M5a1 and GM236"]}]}],"canonical_facts":{"dc:contributor":["Junichi Ryu","Leonard R. Bullas","Kelvin A. W. Hill","John J. Rossi","Anthony J. Zuccarelli"],"dc:creator":["Lee, Nan Sook"],"dc:description.abstract":["Two possible type I restriction-modification (R-M) systems, KpnAI and KpnBl, were recognized in Klebsiella pneumoniae strains M5al and GM236, respectively. In this project, four hsdRKpnAI clones (pNLA1 to pNLA4) were obtained by using an endonuclease expression-selection method. The hsdRKpnAI gene was identified on a 3.6 kb Sau3Al fragment. To map the gene, the hsdRKpnAI clone was hybridized to a membrane which contained pulsed-field gel electrophoresed fragments of the chromosome of the strain M5al. The hsdRKpnAI clone was hybridized to a 19 kb Xbal fragment and a 420 kb Blnl fragment, located at about 16 to 20 min on the recently constructed physical map of the M5al chromosome.
Similarly, the hsdRKpnBI clone was hybridized to a 40 kb Xbal fragment and a 330 kb Blnl fragment of the GM236 chromosome. Among five subclones (pNLB1 to pNLB5), the 3.5 kb BamHI-EcoRl fragment of pNLB2 was the smallest DNA fragment to retain restriction activity through complementation testing. The DNA sequence of the 3.5 kb fragment was determined. An open reading frame (ORF) of 3,039 bp was concluded to be the coding region for the HsdRkpnBI polypeptide. The 1,013 amino acid product (111,430 daltons) deduced from the nucleotide sequence is in excellent agreement with the 116 kD size estimated from the electrophoretic mobility of the putative HsdRkpnBI protein in SDS polyacrylamide gels. The nucleotide sequence of the hsdRkpnBI gene showed no significant similarity to any other sequence in the GenBank database. However, a homology search of the amino acid sequence scored highly with EcoR124/3I, a type IC restriction enzyme. After alignment of the two proteins, two ATP binding domains, a DNA binding domain and seven helicase motifs were found. Eight small ORFs were identified within a few kb on either side of the hsdRKpnBI gene. When subcloned, none of these ORFs showed any modification activity. However, complementation with r-KpnBI m-KpnBI mutant suggests that one downstream ORF is a positive effector for expression of the KpnBI modification activity.
"],"dc:identifier":["https://scholarsrepository.llu.edu/etd/1404"],"dc:language":["English"],"dc:rights":["This title appears here courtesy of the author, who has granted Loma Linda University a limited, non-exclusive right to make this publication available to the public. The author retains all other copyrights."],"dc:subject":["Microbiology","Klebsiella pneumoniae -- genetics; Restriction Mapping Cloning; Molecular"],"dc:title":["Molecular Studies of KpnAI and KpnBI R-M Systems : in KLEBSIELLA PNEUMONIAE M5a1 and GM236"],"thesis:degree_discipline":["Microbiology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Doctor of Philosophy (Medical Science)"]},"updated_at":"2026-07-24T02:53:44Z"}