A Novel H-NS-like Protein from an Antarctic Psychrophilic Bacterium Reveals a Crucial Role for the N-terminal Domain in Thermal Stability*

Christian Tendeng {ddagger} §, Evelyne Krin {ddagger}, Olga A. Soutourina ¶, Antoine Marin ||, Antoine Danchin {ddagger} ** and Philippe N. Bertin {ddagger}{ddagger} §§

From the {ddagger} Unité de Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France, Laboratoire de Biochimie, Ecole Polytechnique, 91128 Palaiseau Cedex, France, || Atelier de Bio-informatique, Université Paris 6, 12 rue Cuvier, 75005 Paris, France, ** HKU-Pasteur Research Centre, Dexter HC Man Building, 8 Sassoon Road, Pokfulam, Hong Kong, China, {ddagger}{ddagger} Laboratoire de Dynamique, Evolution et Expression de Génomes de Microorganismes, FRE 2326, Université Louis Pasteur/CNRS, 67083 Strasbourg Cedex, France

Received for publication, November 19, 2002 , and in revised form, February 24, 2003.
    ABSTRACT
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
We describe here new members of the H-NS protein family identified in a psychrotrophic Acinetobacter spp. bacterium collected in Siberia and in a psychrophilic Psychrobacter spp. bacterium collected in Antarctica. Both are phylogenetically closely related to the HvrA and SPB Rhodobacter transcriptional regulators. Their amino acid sequence shares 40% identity, and their predicted secondary structure displays a structural and functional organization in two modules similar to that of H-NS in Escherichia coli. Remarkably, the Acinetobacter protein fully restores to the wild-type H-NS-dependent phenotypes, whereas the Psychrobacter protein is no longer able to reverse the effects of H-NS deficiency in an E. coli mutant strain above 30 °C. Moreover, in vitro experiments demonstrate that the ability of the Psychrobacter H-NS protein to bind curved DNA and to form dimers is altered at 37 °C. The construction of hybrid proteins containing the N- or the C-terminal part of E. coli H-NS fused to the C- or N-terminal part of the Psychrobacter protein demonstrates the role of the N-terminal domain in this process. Finally, circular dichroism analysis of purified H-NS proteins suggests that, as compared with the E. coli and Acinetobacter proteins, the {alpha}-helical domain displays weaker intermolecular interactions in the Psychrobacter protein, which may account for the low thermal stability observed at 37 °C.


    INTRODUCTION
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Life in cold habitats imposes numerous constraints on bacterial metabolism. These conditions require appropriate adaptation of the structure and the physiology of psychrophilic or psychrotolerant bacteria (1, 2). For instance, the mechanisms allowing these organisms to adapt to low temperature include enhancement of membrane fluidity, which can be obtained through a relative increase in polyunsaturated fatty acids (1, 3). Furthermore, to circumvent the limitations imposed by a reduced thermal energy, enzymatic proteins with a high specific activity are produced (4). At the molecular level, all proteins from psychrotrophic organisms studied so far have shown a decrease in their intramolecular interactions, usually associated with both higher flexibility and lower thermal stability as compared with their mesophilic or thermophilic counterparts (5). Most of the data about the molecular adaptation of proteins to low temperature concern psychrophilic enzymes (4). In contrast, little is known about regulators of gene expression (6, 7), including nucleoid-associated proteins.

The increasing number of sequencing projects has recently revealed the existence of several H-NS-related proteins in Gram-negative bacteria with different life style such as the human pathogenic bacteria Yersinia pestis (8) and Pasteurella multocida (9) and the plant pathogenic bacteria Xylella fastidiosa (10) and Ralstonia solanacearum (11). Some of these proteins have been studied in detail, e.g. those from Vibrio cholerae (12) and Bordetella pertussis (13). All H-NS proteins share the same structural and functional organization in two modules (14, 15). In enterobacteria, the N-terminal domain of H-NS has been recently shown to contain three {alpha}-helices (16), whereas the C-terminal three-dimensional structure of the protein resolved by NMR consists of a mix of {alpha}-{beta} structures (17). The H-NS protein forms oligomers via its N-terminal part and is able to bind curved and AT-rich DNA fragments via its C-terminal domain (18), both essential properties of H-NS and related proteins (19). Nevertheless, the role of most proteins of the H-NS family in bacterial physiology remains unknown (15). In contrast, in Escherichia coli and Salmonella typhimurium H-NS seem to be involved in bacterial nucleoid organization and in the regulation of various genes involved in adaptation to environmental challenges (20, 21). A variety of phenotypes has been associated with a mutation in hns, in particular an increase in pH resistance (21, 22) and a loss of motility (23, 24). Finally, in enterobacteria and related micro-organisms, H-NS proteins are cold shock proteins (12, 25), which could explain the susceptibility to low temperature of E. coli hns mutant (26).

To further investigate the structure-function-evolution relationship of H-NS-related proteins, we identified and characterized orthologous proteins in bacteria isolated from extreme environments, i.e. a psychrotrophic bacterium Acinetobacter spp. isolated from Lake Baikal in Siberia1 and a psychrophilic bacterium Psychrobacter spp. collected from Antarctica (27). Like the protein of E. coli, H-NS-like proteins of Psychrobacter and Acinetobacter were both able to complement H-NS-related phenotypes in E. coli at 30 °C. Surprisingly, the Psychrobacter H-NS protein was no longer able to reverse the effects of H-NS deficiency at 37 °C. In vivo and in vitro experiments demonstrated the crucial role of the N-terminal part on the thermal stability of this unusual H-NS protein and give new insight concerning the structural and functional organization of the proteins of this family.


    MATERIALS AND METHODS
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Bacterial Strains, Growth Conditions, and Plasmids—The Psychrobacter TAD1 strain was grown at various temperatures (from 4 to 25 °C) in Luria-Bertani (LB) medium. The Acinetobacter bacterial strain 20 was grown from 4 to 37 °C in LB medium. E. coli FB8 strain (28) and BE1410, its hns-1001 derivative (29), were used in this study. This H-NS-deficient strain contains a Tn5seq1 transposon insertion located in the 20th codon of the hns gene (30). E. coli cells were grown at various temperatures (from 20 to 37 °C) in LB medium or in M63 medium (31) supplemented with 40 µg/ml serine, 1 mM isopropyl-1-thio-{beta}-D-galactopyranoside, and 0.4% glucose as a carbon source.

Metabolism of {beta}-glucosides was tested on MacConkey agar indicator plates with 1% salicin as a carbon source. Tryptone swarm plates containing 1% Bacto-tryptone, 0.5% NaCl, and 0.3% Bacto-agar were used to test bacterial motility as previously described (23). When required, ampicillin or chloramphenicol was added at 100 µg/ml and 20 µg/ml, respectively. Ultracompetent XL1-Blue (Stratagene) cells were used to construct the genomic library of Acinetobacter 20 and Psychrobacter TAD1 strains. All experiments were performed in accordance with the European requirements for the contained use of genetically modified organisms of Group-I (agreement number 2735) and Group-II (agreement 2736 CAI).

Plasmid pDIA572 was isolated from a Psychrobacter TAD1 genomic library (see below) and carries a DNA fragment of 1330 bp. The insert nucleotide sequence was determined on both strands. The DNA fragment of pDIA572 contains the hns gene of Psychrobacter TAD1 and its flanking regions (accession number AJ310993 [GenBank] ). Plasmid pDIA585 carries a 2673-bp DNA fragment containing the hns gene of Acinetobacter strain 20 and its flanking regions (accession number AJ458445 [GenBank] ). To overproduce the H-NS-His6 proteins of E. coli, Acinetobacter 20, and Psychrobacter TAD1 strains, their structural gene was amplified from genomic DNA using primers 5'-GGAGGTTCATATGAGCGAAGCACTTAAAAT-3' and 5'-CCGCTCGAGTTGCTTGATCAGGAAATCGT-3', primers 5'-GGAGGTTCATATGCCAGATATTAGTAATTTATCTG-3' and 5'-CCGCTCGAGGATGAGGAAGTCTTCCAGTTTCGCACC-3', and primers 5'-GGAGGTTCATATGACTAATAACACTACTAT-3' and 5'-CCGCTCGAGTACAGTAAAACTTTCTAGGT-3', respectively. These pairs of primers introduced a NdeI cloning site and a XhoI cloning site at 5'- and 3'-end, respectively. The PCR products were inserted into the NdeI and XhoI sites of the pET-22b vector (Novagen), giving rise to plasmids pDIA569 (which contains the hns gene of E. coli), pDIA588 (which contains the orthologous gene of Acinetobacter strain 20), and pDIA568 (which contains the orthologous gene of Psychrobacter TAD1).

The genes coding for the H-NS chimeric proteins of E. coli and Psychrobacter TAD1 were constructed as follows. The promoter region and the 5'-end of the hns gene of E. coli were amplified from plasmid pDIA547 (19) using primers 5'-GTTTTCCCAGTCACGAC-3' and 5'-AGATTTAACGGCAGCAAGGC-3' and its 3'-end using primers 5'-TAGAAGAGATTTTGAAGGCTGGCACCAAAGCTAAACGTGC-3' and 5'-AGCGGATAACAATTTCACACAGGA-3'; the 5'-end of the hns gene of Psychrobacter spp. was amplified from plasmid pDIA580 using primers 5'-ATGACTAATAACACTAC-3' and 5'-AGCCTTCAAAATCTCTTCTA-3' and its 3'-end using primers 5'-GCCTTGCTGCCGTTAAATCTGGTGAAAGCCTAGAGAAAAAACG-3' and 5'-CCCAAGCTTGGGTTATACAGTAAAACTTTCTAGG-3'. All constructs were inserted into the HindIII and EcoRI restriction sites of plasmid pDIA547 and gave rise to plasmids pDIA580, pDIA581, and pDIA582 (Table III).


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TABLE III
Effect of temperature on the in vivo complementation of H-NS deficiency in an E. coli hns strain by wild-type and hybrid hns genes

 

Construction of Genomic DNA Libraries—Genomic DNA was isolated from Acinetobacter 20 and Psychrobacter TAD1 bacterial strains. The Psychrobacter genomic library was constructed in plasmid pcDNA 2.1 (Invitrogen) as previously described (15), whereas the Acinetobacter genomic library was constructed in plasmid pDIA561 (21). About 60,000 clones were selected on LB plates supplemented with 100 µg/ml ampicillin or 20 µg/ml chloramphenicol and pooled. Large scale plasmid DNA isolation was carried out using the JETstar kit (GENOMED).

Protein Purification—The recombinant H-NS-His6 proteins of E. coli and Psychrobacter TAD1 strains were purified from E. coli BL21 (DE3) (Stratagene) carrying pDIA17 and pDIA569 or pDIA568 using NiSO4 chelation columns (Qiagen), as previously described (19).

Gel Retardation Experiments—Gel retardation experiments were performed as previously described (23), with H-NS-purified protein of Psychrobacter TAD1 either at 4 or 37 °C. Restriction fragments derived from plasmid pDIA525 that contain flhDC or bla DNA fragments of E. coli were used as competitors.

Protein-Protein Cross-linking—Cross-linking experiments were performed as previously described (12) with 25 µM H-NS of Psychrobacter TAD1 used in each reaction. After adding cross-linking reagents, i.e. 200 mM 1-ethyl-3(3-dimethylaminopropyl)carbodiimide and 50 mM N-hydroxysuccinimide, the reaction mixtures were incubated for 1 h either at 4 °Corat37 °C, loaded onto a SDS-14% Prosieve acrylamide gel, and silver-stained.

Circular Dichroism (CD) Spectroscopy—CD spectra were obtained with a Jobin-Yvon CD6 dichrograph equipped with a thermostatted cell holder. The CD spectra were recorded between 190 and 260 nm from 4 to 70 °C (after 10 min of temperature equilibration before recording the data). The results are the mean values of two successive spectra. CD spectra of purified proteins were determined in pure water with a protein concentration of 14 µM.

In Silico Sequence Analysis—The ProtParam software on the Ex-PASy web site (www.expasy.org/tools/protparam.html) was used to determine the amino acid composition of proteins. The CLUSTALw method (32) was used for sequence alignments. Secondary structure prediction was performed using the PREDATOR method (33), available on the web site pbil.univ-lyon1.fr. The fold recognition method FROST (Fold Recognition Oriented Search Tool), available on the web site www-mig.jouy.inra.fr/mig/index.html, was used for fold assignments to H-NS protein sequences (34).

Nucleotide Sequence Accession Numbers—The nucleotide sequences of 16 S rRNA and hns genes from Psychrobacter TAD1 bacterial strain have been assigned EMBL nucleotide sequence data base accession numbers AJ310992 [GenBank] and AJ310993 [GenBank] , respectively. The 1379 nucleotide sequence of 16 S rRNA gene of Acinetobacter strain 20 was in accordance with the partial sequence in databases under accession number AJ222834 [GenBank] . The Acinetobacter spp. hns gene and its product have been assigned EMBL accession number AJ458445 [GenBank] .


    RESULTS
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Characterization of Natural Bacterial Isolates from Siberia and Antarctica—Two Gram-negative bacteria were isolated from lake Baikal in Siberia and from frozen water in Antarctica. The first strain was isolated from samples collected from the central basin at about 1,000 m below the surface of the lake (35). The selected strain was able to grow under a wide range of temperatures extending from 4 to 37 °C but with an optimum growth temperature of 25 °C. Morphological, biochemical, and phenotypic characterization, e.g. rods occurring in pairs, non-motile bacterium, oxidase-negative and catalase-positive, suggest that this strain belongs to the Acinetobacter genus. Its taxonomic position was further investigated by determination of 16 S rRNA gene sequence (accession number AJ222834 [GenBank] ) and comparative analysis with different DNA sequences present in databases. The construction of a phylogenetic tree further supports the phylogenetic position of this strain, largely in accordance with morphological characterizations, and suggests that Acinetobacter spp. was closely related to Acinetobacter lwoffii A382 and Acinetobacter johnsonii ATCC 17979 (data not shown).

The second strain was collected from frozen continental water in Terre Adélie in Antarctica by C. Gerday, as previously mentioned (27). The morphological and biochemical characteristics of this strain, e.g. coccoid occurring in pairs, oxidase- and catalase-positive, nonmotile bacterium, and growth at low temperatures from 0 to 25 °C with an optimum growth temperature close to 15 °C, indicate that it could be classified either in Moraxella or Psychrobacter groups in agreement with recent data (36). Sequence analysis of the 16 S rDNA (accession number AJ310992 [GenBank] ) together with other characteristics of TAD1 bacterial strain such as a tolerance to 8% NaCl and a susceptibility to bile salt allowed us to refine the classification of this bacterium within the Psychrobacter genus and indicated that this strain could be related to Psychrobacter phenotypic group 2 (phenon 2), which is represented by Psychrobacter uratovorans (37).

Isolation and Characterization of Cold-adapted H-NS-like Proteins—To isolate a putative hns-like gene from both bacterial strains, we took advantage of the serine susceptibility of hns mutants in E. coli (38). A genomic library was constructed for both strains (see "Materials and Methods"), and each of them was introduced into the hns E. coli strain BE1410. The selection was performed on minimal medium supplemented with serine, as previously described (12, 15). Several clones were screened at 20 °C for 3 additional phenotypes, i.e. swarming on semi-solid medium, {beta}-glucoside metabolism on MacConkey agar plate, and mucoidy on rich medium.

Analysis of the nucleotide sequence of different plasmid DNA inserts revealed the presence of a coding sequence of 321 bp, coding for a 107-amino acid protein with a predicted molecular mass of about 12 kDa and a pI of about 8 in both organisms. The analysis of flanking regions suggests that both genes are not part of a polycistronic operon. As compared with the E. coli H-NS, the modification in the amino acid composition, e.g. the proline content, of the Psychrobacter spp. orthologous protein (Table I) seemed to be similar to that commonly observed from mesophilic to psychrophilic proteins (39). Multiple alignment with various H-NS-related proteins revealed that both cold-adapted proteins share 40% amino acid identity in common; they also showed more than 30% identity with the H-NS-related proteins of Rhodobacter species, i.e. HvrA and SPB, and less than 20% with the E. coli H-NS amino acid sequence (Fig. 1). Despite this, the N-terminal part of these two new proteins was predicted to adopt an {alpha}-helical structure, like H-NS in E. coli (data not shown). Moreover, the Acinetobacter H-NS protein displayed the H-NS consensus motif, i.e. YX6(G/S)-(E/D)X(0/2)TW(T/S)G(Q/R)G(R/K)XPX(4/5)AX(3/4)G (0/2, 4/5, and 3/4 indicate 0 or 2, 4 or 5, and 3 or 4 residue(s), respectively) (15), whereas the (G/S) residue was replaced by an asparagine in the Psychrobacter protein (Fig. 1). Finally, using FROST, both C-terminal domains were clearly predicted to share a similar three-dimensional structure with the E. coli H-NS protein, with an error rate lower than 1% as indicated by the normalized distances obtained, i.e. 7.5 and 8.1, respectively, for the Acinetobacter and Psychrobacter proteins (34).


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TABLE I
Amino acid composition of E. coli, Acinetobacter spp., and Psychrobacter spp.

 


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FIG. 1.
Structurally based alignment of H-NS proteins of E. coli (ecoli), Rhodobacter capsulatus (rhoca), Rhodobacter sphaeroides (rhosp), Acinetobacter spp. (acisp), and Psychrobacter spp (psysp). The alignment was achieved using CLUSTALw (32) and refined manually. Residues conserved in at least three sequences are in gray boxes, and the C-terminal domain of H-NS and related proteins (19) is underlined.

 

Effect of a Moderate Temperature Increase on in Vivo Biological Activity and in Vitro Biochemical Properties of the Psychrobacter H-NS Protein—Because of the low growth temperature optimum of both Acinetobacter spp. and Psychrobacter spp. strains, the ability of their H-NS-like proteins to complement phenotypes of E. coli hns mutant was evaluated at various temperatures. Remarkably, the overexpression of Acinetobacter protein fully restored, like the E. coli H-NS protein, a wild-type phenotype with regard to {beta}-glucoside utilization and mucoidy at all temperatures tested, whereas the Psychrobacter H-NS protein was no longer able to reverse the effects of H-NS deficiency in an E. coli mutant strain above 30 °C (Table II). This loss of in vivo complementation observed above 30 °C did not result from the proteolysis of the protein. Indeed, the over-expressed H-NS protein of Psychrobacter was visualized on a polyacrylamide gel after extraction from E. coli hns cells grown at 37 °C (data not shown). This observation prompted us to further examine the biochemical properties of purified Psychrobacter H-NS protein at various temperatures.


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TABLE II
Effect of temperature on the in vivo complementation of H-NS deficiency in an E. coli mutant strain by hns genes of Acinetobacter spp. or Psychrobacter spp.

 

One of the most important functions of H-NS-like proteins is their ability to bind curved DNA (18). Therefore, the binding properties of a recombinant His-6 Psychrobacter H-NS protein was analyzed at 4 and 37 °C in gel retardation experiments. As compared with the 400-bp DNA fragment used as a control, a full retardation in the electrophoretic mobility of both flhDC and bla curved DNA fragments was observed at 4 °C at a protein concentration of 0.25 µM (Fig. 2). No such retardation was detected at 37 °C at the same concentration (Fig. 2). Nevertheless, an increase in the concentration of the protein up to 1 µM resulted in a specific retardation of both curved DNA fragments at 37 °C (Fig. 2).



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FIG. 2.
Effect of temperature on DNA binding evaluated by competitive gel retardation assay with the Psychrobacter H-NS His-6 protein and restriction fragments derived from plasmid pDIA525, which contains flhDC and bla promoter regions. These DNA fragments were incubated with the indicated protein concentration at 4 and 37 °C.

 

The H-NS activity also relies on its propensity to form oligomers (40). Therefore, the ability of the Psychrobacter H-NS protein to oligomerize in vitro was analyzed by cross-linking experiments at 4 and 37 °C (Fig. 3). After a 60-min incubation, the protein was able to form oligomers at 4 °C in the presence of linking reagents (Fig. 3). In contrast, only a residual amount of protein oligomerized as dimers at 37 °C. In addition, no higher order form was observed as compared with those visualized at 4 °C (Fig. 3).



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FIG. 3.
Effect of temperature on protein oligomerization evaluated by in vitro chemical cross-linking experiments using Psychrobacter His-6 protein. After 1 h of incubation at 4 and 37 °C with (+) or without (–) 1-ethyl-3(3-dimethylaminopropyl)carbodiimide-N-hydroxysuccinimide cross-linking reagents, proteins were loaded onto a SDS, 14% acrylamide gel and silver-stained.

 

The Low Thermal Stability of the Psychrobacter H-NS Protein Depends on the N-terminal Domain—The loss of Psychrobacter H-NS protein activity in vivo could result from an altered conformation during a moderate temperature increase. To evaluate the role of the different domains of the Psychrobacter protein in its thermosensitivity, we constructed different chimeric proteins with either the N- or the C-terminal part of E. coli H-NS fused to the C- or N-terminal part of the Psychrobacter protein (see "Materials and Methods"). To rule out any effect of temperature above 30 °C on Psychrobacter hns gene expression, all constructs were placed under the same transcriptional control of the E. coli hns promoter, giving rise to three plasmids (Table III) pDIA580 (producing the Psychrobacter wild-type H-NS protein), pDIA581 (producing a chimeric protein containing the N-terminal part of the E. coli H-NS and the C-terminal domain of the Psychrobacter protein), and pDIA582 (producing a chimeric protein containing the N-terminal part of the Psychrobacter protein and the C-terminal domain of the E. coli H-NS).

These plasmids were used in in vivo complementation experiments at two different temperatures, i.e. 25 and 37 °C. The synthesis of a chimeric protein containing the N-terminal part of the Psychrobacter H-NS protein (i.e. from plasmid pDIA582) in the hns E. coli mutant strain restored the wild-type phenotypes at 25 °C but not at 37 °C, as observed with the wild-type Psychrobacter protein from plasmid pDIA580 (Tables II and III). In contrast, the synthesis of a chimeric protein containing the N-terminal part of the E. coli H-NS protein fused to the Psychrobacter C-terminal domain (i.e. from plasmid pDIA581) fully reversed the effects of H-NS deficiency in an E. coli hns mutant also at 37 °C (Table III).

Biophysical Properties of the Psychrobacter H-NS, a Thermosensitive Protein—The influence of an increase in temperature on the conformation of the Psychrobacter H-NS protein was evaluated by CD spectroscopy (41). Below 25 °C, the spectra of the protein revealed the presence of 1 positive maximum band at 190 nm and of 2 negative maxima bands at 208 and 222 nm, indicating the existence of a large proportion of {alpha}-helix structures (Fig. 4A). As a control, CD analyses of the E. coli H-NS protein also revealed the existence of a large portion of {alpha}-helix structures (data not shown), which mainly reflect the secondary structure of its N-terminal part, in agreement with recent results (40). In contrast, unlike both the E. coli (data not shown) and the Acinetobacter (Fig. 4B) H-NS proteins, a moderate increase in temperature led to a complete change in CD profile of the Psychrobacter H-NS protein. The presence of an isodichroic point at 202 nm indicated a transition from the {alpha}-helix structures toward random coils (Fig. 4A). In addition, the CD profile did not revert to the native spectrum after a temperature down-shift from 50 to 20 °C, and after cooling the CD profile remained similar to that observed above 30 °C (Fig. 4A), providing evidence that, unlike E. coli H-NS (40, 42) and Acinetobacter H-NS (Fig. 4B), the perturbation observed was irreversible. Finally, from the sigmoidal shape of the denaturation curve resulting from the CD spectra, we could determine a melting temperature (Tm) of 21 °C, which further supports the low thermal stability of the Psychrobacter H-NS protein (Fig. 5).



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FIG. 4.
Effect of temperature on secondary structure of H-NS proteins visualized by CD spectroscopy. A, CD spectra of the Psychrobacter H-NS obtained with 14 µM protein at different temperatures, i.e. 3 °C(solid line), 21 °C(broken line), and 35 °C(dotted line). B, given in the inset are the CD spectra at 3 °C (solid line), 21 °C (broken line), and 35 °C (dotted line) of the Acinetobacter H-NS protein.

 


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FIG. 5.
Sigmoid curve of the Psychrobacter H-NS resulting from CD spectra between 6 and 35 °C. The curve allowed the determination of a Tm of 21 °C.

 


    DISCUSSION
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Many adaptations in the structure and the physiology of organisms are required to sustain growth in cold environments (3). Although the properties of psychrophilic enzymes have been well studied at the molecular level (4), almost no information is available about nucleoid-associated proteins from psychrophilic organisms. In this work, we isolated and characterized two hns genes from two cold-adapted bacteria, i.e. Acinetobacter spp. and Psychrobacter spp. Each gene codes for a 107-amino acid protein with more than 30% identity with the H-NS-like proteins of Rhodobacter species, i.e. HvrA and SPB, and less than 20% with the E. coli H-NS amino acid sequence (Fig. 1). Nevertheless, in silico analysis suggests that both Acinetobacter and Psychrobacter proteins display the typical structural and functional organization in two modules observed in other H-NS-related proteins (14, 15, 19). Indeed, the N-terminal part is predicted to mainly adopt an {alpha}-helix conformation, whereas as predicted by the fold recognition method FROST, the C-terminal domain shares a similar three-dimensional structure with the E. coli H-NS protein resolved by NMR (see "Results") (17). These predictions were substantiated by the ability of both proteins to complement hns phenotypes in a hns-defective E. coli mutant (Table II), including a restoration of motility although Acinetobacter spp. and Psychrobacter spp. strains are non-motile (data not shown). These results provide evidence that the two proteins identified in this work belong to the H-NS family and are the first members of this family isolated from cold-adapted bacteria. In contrast, no H-NS-related protein has been so far identified in hyperthermophiles bacteria whose genome has been recently sequenced (igweb.integratedgenomics.com/GOLD).

The catalytic activity of psychrophilic enzymes is known to decrease dramatically as the temperature increases (4). For instance, the activity of a {alpha}-amylase enzyme secreted by the Antarctic bacterial strain Alteromonas haloplanctis decreases above 25 °C because of a low thermal stability, whereas a homologous protein of pig pancreas displays an optimum activity at 60 °C (43). This low thermal stability in psychrophilic enzymes, which is often considered as a consequence of higher flexibility and catalytic activity, results from a decrease in electrostatic and hydrophobic interactions (5, 44). Usually various modifications are observed when psychrophilic proteins are compared with their mesophilic counterparts, such as a decrease of charged residues, a substitution of hydrophobic residues, e.g. Ala instead of Val, or a decrease in proline content (39). In this respect, as compared with the E. coli H-NS protein, the aspartate and valine content was decreased in the Psychrobacter H-NS protein sequence (Table I). Recent results show that the substitution of two alanines by two threonines and one alanine by one valine could create a psychrophilic-like subtilisin from a mesophilic enzyme (45). Interestingly, the threonine content increases in the Psychrobacter H-NS protein as compared with the orthologous protein in E. coli. In addition, the asparagine content, which is considered as a thermolabile residue (46), is increased in the Psychrobacter protein. No such differences were observed in the sequence of the Acinetobacter H-NS protein (Table I). Finally, the Psychrobacter H-NS protein has the lowest proline content, i.e. one proline residue (Fig. 1), as compared with all H-NS-related proteins identified so far. This proline residue, which is located in the C-terminal domain, corresponds to the Pro-115 residue in E. coli. In this organism, this proline has been suggested to play a crucial role in oligomer formation despite its location in the DNA binding domain (47). Although this proline residue could also be involved in the oligomerization of other H-NS proteins, its presence is not sufficient to confer a thermal stability to the H-NS protein of Psychrobacter. In this respect, we were not able to create a mesophilic-like protein from H-NS of Psychrobacter spp. by random mutagenesis experiments,2 suggesting that more than one amino acid modification is involved in its structural adaptation to low temperature.

The Acinetobacter H-NS protein fully restored to the wild type H-NS-dependent phenotypes at all temperatures tested although the Psychrobacter H-NS protein was no longer able to reverse the effects of H-NS deficiency in an E. coli mutant strain above 30 °C (Table II). Moreover, the Psychrobacter H-NS protein could no longer bind curved DNA fragments at 37 °C excepted at a concentration of 1 µM (Fig. 2). In contrast, no oligomer form could be visualized at the same temperature even with a protein concentration of 25 µM (Fig. 3). This suggests that, like the H-NS protein of E. coli (48), the Psychrobacter protein could bind curved DNA as a monomer although with a lower efficiency. More importantly, these observations suggest that the effect of an increase in temperature results in an alteration of the conformation of the N-terminal domain. The construction of chimeric proteins between the H-NS protein of E. coli and the orthologous protein of Psychrobacter supports this hypothesis. Indeed, the protein containing the N-terminal part of the Psychrobacter H-NS combined with the C-terminal part of the E. coli H-NS restored the wild-type phenotypes at 25 °C but not at 37 °C (Table III). In contrast, the protein containing the N-terminal part of E. coli H-NS fused to the C-terminal part of the Psychrobacter protein reversed the effects of H-NS deficiency in an hns E. coli mutant strain at 37 °C (Table III). These results clearly demonstrated that the organization of N-terminal domain of the Psychrobacter protein may account for the low thermal stability of this H-NS-like protein.

In S. typhimurium, the N-terminal domain of H-NS has been recently shown to contain three {alpha}-helical regions (16). The authors proposed a model of global topological fold for the N-terminal domain; the third and longest {alpha}-helix forms the core of a coiled-coil configuration, whereas the two others stabilize the structure (16). Secondary structure prediction methods clearly suggest that the Psychrobacter H-NS protein characterized in the present study contain less than three {alpha}-helical regions (data not shown). It is, therefore, tempting to speculate that the amino acid modifications and the different {alpha}-helix organization observed in its N-terminal domain as compared with that of the orthologous E. coli protein reflect a structural adaptation to low temperature of the Psychrobacter H-NS protein. These features might, therefore, offer weaker intermolecular interactions as compared with other H-NS proteins such as those of Acinetobacter and E. coli (or S. typhimurium). CD analyses performed with the Psychrobacter H-NS protein in comparison with the E. coli and Acinetobacter H-NS proteins support this hypothesis (Fig. 4). Indeed, unlike the E. coli protein, which has been isolated more than 30 years ago as a heat-stable factor (49), and the Acinetobacter H-NS protein (Fig. 4B), the {alpha}-helical structure of the Psychrobacter protein was irreversibly denatured upon a moderate temperature increase (Fig. 4A). In addition, although the Tm of the E. coli H-NS protein was estimated around 60 °C (40, 42) and that of Acinetobacter H-NS around 40 °C (data not shown), we could clearly determine the Tm of the Psychrobacter H-NS protein, i.e. 21 °C (Fig. 5). This Tm value is significantly lower than that of both E. coli and Acinetobacter H-NS proteins and may explain the temperature effect observed in vitro and in vivo with the Psychrobacter H-NS protein. A moderate temperature increase could, therefore, easily disassociate oligomers with a subsequent and/or concomitant irreversible denaturation of the protein, as observed by CD analysis. We can hypothesize from these results that the organization of {alpha}-helix structures in the N-terminal domain is crucial for the structure and the function of H-NS-related proteins. Hence, the identification and characterization of proteins from micro-organisms phylogenetically distant and/or with very different live style, including extremophiles, may lead to a better understanding of the structure, function and evolution relationship of this family of enigmatic proteins.


    FOOTNOTES
 
* This work was supported by the Institut Pasteur and CNRS Grants URA1129 and URA 2171. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. Back

§ Supported by Ministère de l'Enseignement Supérieur et de la Recherche grants. Back

§§ To whom correspondence should be addressed: Laboratoire de Dynamique, Evolution et Expression de Génomes de Microorganismes, Université Louis Pasteur, 28 rue Goethe, 67000 Strasbourg, France. Tel.: 33-3-19-24-20-08; Fax: 33-3-19-24-20-28; E-mail: bertin{at}gem.u-strasbg.fr.

1 L. Denissova, unpublished data. Back

2 C. Tendeng, E. Krin, O. A. Soutourina, A. Marin, A. Danchin, and P. N. Bertin, unpublished results. Back


    ACKNOWLEDGMENTS
 
Psychrobacter TAD1 strain was kindly provided by Dr. C. Gerday. We are thankful to V. V. Parfenova for providing us with the Baikal bacterial strain and to G. Feller for helpful advice. We are indebted to M. Monot, S. Fermandjian, and M. Nicaise for CD experiments and analyses. We are grateful to J. Potier for helpful advice concerning the protein structure analyses. We thank K. Sun and F. Hommais for technical assistance.



    REFERENCES
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