The thermostability of DNA-binding protein HU from mesophilic, thermophilic, and extreme thermophilic bacteria View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2002-02

AUTHORS

Evangelos Christodoulou, Constantinos E. Vorgias

ABSTRACT

Based on primary structure comparison between four highly homologous DNA-binding proteins (HUs) displaying differential thermostability, we have employed in vitro site-directed mutagenesis to decipher their thermostability mechanism at the molecular level. The contribution of the 11 amino acids that differ between the thermophilic HUBst from Bacillus stearothermophilus (Tm = 61.6 degrees C) and the mesophilic HUBsu from Bacillus subtilis (Tm = 39.7 degrees C) was evaluated by replacing these amino acids in HUBst with their mesophilic counterparts. Among 11 amino acids, three residues, Gly-15, Glu-34, and Val-42, which are highly conserved in the thermophilic HUs, have been found to be responsible for the thermostability of HUBst. These amino acids in combination (HUBst-G15E/E34D/V42I) reduce the thermostability of the protein (Tm = 45.1 degrees C) at the level of its mesophilic homologue HUBsu. By replacing these amino acids in HUBsu with their thermophilic counterparts, the HUBsu-E15G/D34E/142V mutant was generated with thermostability (Tm = 57.8 degrees C) at the level of thermophilic HUBst. Employing the same strategy, we generated several mutants in the extremely thermophilic HUTmar from Thermotoga maritima (Tm = 80.5 degrees C), and obtained data consistent with the previous results. The triplet mutant HUTmar-G15E/E34D/V421 (Tm = 35.9 degrees C) converted the extremely thermophilic protein HUTmar to mesophilic. The various forms of HU proteins were overproduced in Escherichia coli, highly purified, and the thermostability of the mutants confirmed by circular dichroism spectroscopy. The results presented here were elucidated on the basis of the X-ray structure of HUBst and HUTmar (our unpublished results), and their mechanism was proposed at the molecular level. The results clearly show that three individual local interactions located at the helix-turn-helix part of the protein are responsible for the stability of HU proteins by acting cooperatively in a common mechanism for thermostability. More... »

PAGES

21-31

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s007920100235

DOI

http://dx.doi.org/10.1007/s007920100235

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1013991685

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/11878558


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biochemistry and Cell Biology", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Amino Acid Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Bacillus subtilis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Bacteria", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Bacterial Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Crystallography, X-Ray", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA-Binding Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Drug Stability", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Geobacillus stearothermophilus", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Molecular", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Sequence Data", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Mutation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Conformation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Denaturation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Alignment", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Homology, Amino Acid", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Temperature", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Thermodynamics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Transcription Factors", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "National and Kapodistrian University of Athens", 
          "id": "https://www.grid.ac/institutes/grid.5216.0", 
          "name": [
            "Faculty of Biology, Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopoli-Zographou, 15784 Athens, Greece"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Christodoulou", 
        "givenName": "Evangelos", 
        "id": "sg:person.01010102466.94", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01010102466.94"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National and Kapodistrian University of Athens", 
          "id": "https://www.grid.ac/institutes/grid.5216.0", 
          "name": [
            "Faculty of Biology, Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopoli-Zographou, 15784 Athens, Greece"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Vorgias", 
        "givenName": "Constantinos E.", 
        "id": "sg:person.012207207204.84", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012207207204.84"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "2002-02", 
    "datePublishedReg": "2002-02-01", 
    "description": "Based on primary structure comparison between four highly homologous DNA-binding proteins (HUs) displaying differential thermostability, we have employed in vitro site-directed mutagenesis to decipher their thermostability mechanism at the molecular level. The contribution of the 11 amino acids that differ between the thermophilic HUBst from Bacillus stearothermophilus (Tm = 61.6 degrees C) and the mesophilic HUBsu from Bacillus subtilis (Tm = 39.7 degrees C) was evaluated by replacing these amino acids in HUBst with their mesophilic counterparts. Among 11 amino acids, three residues, Gly-15, Glu-34, and Val-42, which are highly conserved in the thermophilic HUs, have been found to be responsible for the thermostability of HUBst. These amino acids in combination (HUBst-G15E/E34D/V42I) reduce the thermostability of the protein (Tm = 45.1 degrees C) at the level of its mesophilic homologue HUBsu. By replacing these amino acids in HUBsu with their thermophilic counterparts, the HUBsu-E15G/D34E/142V mutant was generated with thermostability (Tm = 57.8 degrees C) at the level of thermophilic HUBst. Employing the same strategy, we generated several mutants in the extremely thermophilic HUTmar from Thermotoga maritima (Tm = 80.5 degrees C), and obtained data consistent with the previous results. The triplet mutant HUTmar-G15E/E34D/V421 (Tm = 35.9 degrees C) converted the extremely thermophilic protein HUTmar to mesophilic. The various forms of HU proteins were overproduced in Escherichia coli, highly purified, and the thermostability of the mutants confirmed by circular dichroism spectroscopy. The results presented here were elucidated on the basis of the X-ray structure of HUBst and HUTmar (our unpublished results), and their mechanism was proposed at the molecular level. The results clearly show that three individual local interactions located at the helix-turn-helix part of the protein are responsible for the stability of HU proteins by acting cooperatively in a common mechanism for thermostability.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1007/s007920100235", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1116821", 
        "issn": [
          "1431-0651", 
          "1433-4909"
        ], 
        "name": "Extremophiles", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "6"
      }
    ], 
    "name": "The thermostability of DNA-binding protein HU from mesophilic, thermophilic, and extreme thermophilic bacteria", 
    "pagination": "21-31", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "42a7311301bac90a68f00f24a7fb997a6d4722c6e0add539fc8df43a0f0d06e6"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "11878558"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "9706854"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/s007920100235"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1013991685"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/s007920100235", 
      "https://app.dimensions.ai/details/publication/pub.1013991685"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T15:00", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8663_00000511.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1007%2Fs007920100235"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s007920100235'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s007920100235'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s007920100235'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s007920100235'


 

This table displays all metadata directly associated to this object as RDF triples.

148 TRIPLES      20 PREDICATES      47 URIs      39 LITERALS      27 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/s007920100235 schema:about N086a8cf8b6f24d6e9b43e85004d6c1b7
2 N08ea7d18a9404e40902c0cbe0998477a
3 N1f3524545e3f440887b607d5d9a11e1b
4 N2076c4d3697b4e958aaf17b7468e972d
5 N389de8d7cb50477397ae07066a839066
6 N39271f651d584dec90c254be2980e9e6
7 N48658a5789174b42a4ec3c7ecc39187e
8 N4f2421e6318248408bede6b73055eb14
9 N6d1e6cd89835432d840f51eb9c6300bf
10 N89bcc15619d84ebca5de30508c40025b
11 N9ef4eb355bf64af8be297ea6b6ec8515
12 Na00e0e98419b4a14b2ed6a1e3e073127
13 Na7bbb035ef124d979c12d51f94827870
14 Nb7e7a4e45bef40769fdd1d0aa9a82f10
15 Nb9dcb6e1b3954ad9b736d1f901644e3f
16 Nc2c2ad089d75433bb2975afea3ed6504
17 Nce3ec71699b04a8cb71979319fdee449
18 Nd12c811f65df46c7a068b87540ecf83d
19 anzsrc-for:06
20 anzsrc-for:0601
21 schema:author N54a4afabbe5c483382b61b542e2a8b88
22 schema:datePublished 2002-02
23 schema:datePublishedReg 2002-02-01
24 schema:description Based on primary structure comparison between four highly homologous DNA-binding proteins (HUs) displaying differential thermostability, we have employed in vitro site-directed mutagenesis to decipher their thermostability mechanism at the molecular level. The contribution of the 11 amino acids that differ between the thermophilic HUBst from Bacillus stearothermophilus (Tm = 61.6 degrees C) and the mesophilic HUBsu from Bacillus subtilis (Tm = 39.7 degrees C) was evaluated by replacing these amino acids in HUBst with their mesophilic counterparts. Among 11 amino acids, three residues, Gly-15, Glu-34, and Val-42, which are highly conserved in the thermophilic HUs, have been found to be responsible for the thermostability of HUBst. These amino acids in combination (HUBst-G15E/E34D/V42I) reduce the thermostability of the protein (Tm = 45.1 degrees C) at the level of its mesophilic homologue HUBsu. By replacing these amino acids in HUBsu with their thermophilic counterparts, the HUBsu-E15G/D34E/142V mutant was generated with thermostability (Tm = 57.8 degrees C) at the level of thermophilic HUBst. Employing the same strategy, we generated several mutants in the extremely thermophilic HUTmar from Thermotoga maritima (Tm = 80.5 degrees C), and obtained data consistent with the previous results. The triplet mutant HUTmar-G15E/E34D/V421 (Tm = 35.9 degrees C) converted the extremely thermophilic protein HUTmar to mesophilic. The various forms of HU proteins were overproduced in Escherichia coli, highly purified, and the thermostability of the mutants confirmed by circular dichroism spectroscopy. The results presented here were elucidated on the basis of the X-ray structure of HUBst and HUTmar (our unpublished results), and their mechanism was proposed at the molecular level. The results clearly show that three individual local interactions located at the helix-turn-helix part of the protein are responsible for the stability of HU proteins by acting cooperatively in a common mechanism for thermostability.
25 schema:genre research_article
26 schema:inLanguage en
27 schema:isAccessibleForFree false
28 schema:isPartOf N90457872ce9b4525895c136c9de61538
29 Nf09592aec99d4419ace9eed155b3d534
30 sg:journal.1116821
31 schema:name The thermostability of DNA-binding protein HU from mesophilic, thermophilic, and extreme thermophilic bacteria
32 schema:pagination 21-31
33 schema:productId N42fcb6e73ef846249920c8b87902727a
34 N64eb7c7727d94286b87ccc20ed1b898d
35 N802a29f21ae14d3a93279ba1204e5be7
36 N81ad442444474994b54f1816570fa1fd
37 N8e208f68775d4713b82dc37583ca2338
38 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013991685
39 https://doi.org/10.1007/s007920100235
40 schema:sdDatePublished 2019-04-10T15:00
41 schema:sdLicense https://scigraph.springernature.com/explorer/license/
42 schema:sdPublisher N3ea8c25454864cb981df4ee8b4aaefe5
43 schema:url http://link.springer.com/10.1007%2Fs007920100235
44 sgo:license sg:explorer/license/
45 sgo:sdDataset articles
46 rdf:type schema:ScholarlyArticle
47 N086a8cf8b6f24d6e9b43e85004d6c1b7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
48 schema:name Bacteria
49 rdf:type schema:DefinedTerm
50 N08ea7d18a9404e40902c0cbe0998477a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
51 schema:name Thermodynamics
52 rdf:type schema:DefinedTerm
53 N1f3524545e3f440887b607d5d9a11e1b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
54 schema:name Transcription Factors
55 rdf:type schema:DefinedTerm
56 N2076c4d3697b4e958aaf17b7468e972d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
57 schema:name Temperature
58 rdf:type schema:DefinedTerm
59 N389de8d7cb50477397ae07066a839066 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
60 schema:name Drug Stability
61 rdf:type schema:DefinedTerm
62 N39271f651d584dec90c254be2980e9e6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
63 schema:name Sequence Homology, Amino Acid
64 rdf:type schema:DefinedTerm
65 N3ea8c25454864cb981df4ee8b4aaefe5 schema:name Springer Nature - SN SciGraph project
66 rdf:type schema:Organization
67 N42fcb6e73ef846249920c8b87902727a schema:name readcube_id
68 schema:value 42a7311301bac90a68f00f24a7fb997a6d4722c6e0add539fc8df43a0f0d06e6
69 rdf:type schema:PropertyValue
70 N48658a5789174b42a4ec3c7ecc39187e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
71 schema:name Mutation
72 rdf:type schema:DefinedTerm
73 N4f2421e6318248408bede6b73055eb14 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
74 schema:name Geobacillus stearothermophilus
75 rdf:type schema:DefinedTerm
76 N54a4afabbe5c483382b61b542e2a8b88 rdf:first sg:person.01010102466.94
77 rdf:rest Nfe190dba036e42b3970c827780d95fcb
78 N64eb7c7727d94286b87ccc20ed1b898d schema:name doi
79 schema:value 10.1007/s007920100235
80 rdf:type schema:PropertyValue
81 N6d1e6cd89835432d840f51eb9c6300bf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
82 schema:name Protein Denaturation
83 rdf:type schema:DefinedTerm
84 N802a29f21ae14d3a93279ba1204e5be7 schema:name dimensions_id
85 schema:value pub.1013991685
86 rdf:type schema:PropertyValue
87 N81ad442444474994b54f1816570fa1fd schema:name nlm_unique_id
88 schema:value 9706854
89 rdf:type schema:PropertyValue
90 N89bcc15619d84ebca5de30508c40025b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
91 schema:name Protein Conformation
92 rdf:type schema:DefinedTerm
93 N8e208f68775d4713b82dc37583ca2338 schema:name pubmed_id
94 schema:value 11878558
95 rdf:type schema:PropertyValue
96 N90457872ce9b4525895c136c9de61538 schema:issueNumber 1
97 rdf:type schema:PublicationIssue
98 N9ef4eb355bf64af8be297ea6b6ec8515 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
99 schema:name Bacterial Proteins
100 rdf:type schema:DefinedTerm
101 Na00e0e98419b4a14b2ed6a1e3e073127 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
102 schema:name Bacillus subtilis
103 rdf:type schema:DefinedTerm
104 Na7bbb035ef124d979c12d51f94827870 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
105 schema:name Amino Acid Sequence
106 rdf:type schema:DefinedTerm
107 Nb7e7a4e45bef40769fdd1d0aa9a82f10 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
108 schema:name Sequence Alignment
109 rdf:type schema:DefinedTerm
110 Nb9dcb6e1b3954ad9b736d1f901644e3f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
111 schema:name DNA-Binding Proteins
112 rdf:type schema:DefinedTerm
113 Nc2c2ad089d75433bb2975afea3ed6504 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
114 schema:name Crystallography, X-Ray
115 rdf:type schema:DefinedTerm
116 Nce3ec71699b04a8cb71979319fdee449 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
117 schema:name Molecular Sequence Data
118 rdf:type schema:DefinedTerm
119 Nd12c811f65df46c7a068b87540ecf83d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
120 schema:name Models, Molecular
121 rdf:type schema:DefinedTerm
122 Nf09592aec99d4419ace9eed155b3d534 schema:volumeNumber 6
123 rdf:type schema:PublicationVolume
124 Nfe190dba036e42b3970c827780d95fcb rdf:first sg:person.012207207204.84
125 rdf:rest rdf:nil
126 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
127 schema:name Biological Sciences
128 rdf:type schema:DefinedTerm
129 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
130 schema:name Biochemistry and Cell Biology
131 rdf:type schema:DefinedTerm
132 sg:journal.1116821 schema:issn 1431-0651
133 1433-4909
134 schema:name Extremophiles
135 rdf:type schema:Periodical
136 sg:person.01010102466.94 schema:affiliation https://www.grid.ac/institutes/grid.5216.0
137 schema:familyName Christodoulou
138 schema:givenName Evangelos
139 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01010102466.94
140 rdf:type schema:Person
141 sg:person.012207207204.84 schema:affiliation https://www.grid.ac/institutes/grid.5216.0
142 schema:familyName Vorgias
143 schema:givenName Constantinos E.
144 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012207207204.84
145 rdf:type schema:Person
146 https://www.grid.ac/institutes/grid.5216.0 schema:alternateName National and Kapodistrian University of Athens
147 schema:name Faculty of Biology, Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopoli-Zographou, 15784 Athens, Greece
148 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...