Escherichia coli ykfE ORFan Gene Encodes a Potent Inhibitor of C-type Lysozyme*

Vincent MonchoisDagger §, Chantal AbergelDagger , James Sturgis, Sandra JeudyDagger , and Jean-Michel ClaverieDagger

From the Dagger  Information Génétique et Structurale, UMR1889 CNRS-AVENTIS and  Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UPR 9027, 31 Chemin Joseph Aiguier, 13402 Marseille, CEDEX 20, France

Received for publication, November 13, 2000, and in revised form, February 22, 2001


    ABSTRACT
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES

The complete nucleotide sequences of over 37 microbial and three eukaryote genomes are already publicly available, and more sequencing is in progress. Despite this accumulation of data, newly sequenced microbial genomes continue to reveal up to 50% of functionally uncharacterized "anonymous" genes. A majority of these anonymous proteins have homologues in other organisms, whereas the rest exhibit no clear similarity to any other sequence in the data bases. This set of unique, apparently species-specific, sequences are referred to as ORFans. The biochemical and structural analysis of ORFan gene products is of both evolutionary and functional interest. Here we report the cloning and expression of Escherichia coli ORFan ykfE gene and the functional characterization of the encoded protein. Under physiological conditions, the protein is a homodimer with a strong affinity for C-type lysozyme, as revealed by co-purification and co-crystallization. Activity measurements and fluorescence studies demonstrated that the YkfE gene product is a potent C-type lysozyme inhibitor (Ki approx  1 nM). To denote this newly assigned function, ykfE has now been registered under the new gene name Ivy (inhibitor of vertebrate lysozyme) at the E. coli genetic stock center.


    INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES

Despite the accumulation of sequence information from a large diversity of species and phyla, newly sequenced bacterial genomes continue to reveal a high proportion of genes of unknown function (1), including a significant subset of "ORFans" (2), i.e. putative open reading frames (ORFs)1 without significant similarity to any previously encountered protein (or conceptual translation) sequences. Most genes found in data bases have only been predicted by computer methods and never experimentally validated. It is thus expected that some annotated ORFs, in particular among the ORFans, might not correspond to real genes. In a previous study, we verified the existence of a cognate transcript for 25 Escherichia coli ORFans with a surprising rate of success (92%) (3). Given that most ORFans appear to be transcribed, we have now initiated a systematic expression and structure determination program for the proteins encoded by these (apparently) unique genes. Because three-dimensional structures are more resilient to evolution and change than amino acid sequences, it is expected that some ORFans should exhibit structural similarity to previously described protein families, hence providing some functional hints. Alternatively, targeting ORFans for structure determination is also a suitable strategy to optimize the discovery of original protein folds, one of the goals of structural genomics.

In a pilot study involving five ORFan genes, we succeeded in producing four of them in E. coli as soluble proteins, and we report here the most advanced project, ykfE. YkfE (Swiss-Prot accession number P45552; b0220 in the Blattner data base (4)) is a 474-nucleotide-long uncharacterized ORF. It is part of a single gene operon and was found to exhibit a high level of expression during the exponential and stationary phases of E. coli growth (3). The ykfE ORF exhibits an N-terminal signal peptide cleaved to produce the mature protein (5, 6). Initial purification steps and biochemical analyses suggested a strong interaction between this protein and hen egg white lysozyme (HEWL). The existence of a stable complex was confirmed by biophysical analyses, and enzymatic studies revealed the capacity of ykfE to inhibit hen and human C-type lysozymes through a specific interaction. The x-ray structure determination of ykfE, both in isolation (7) and in a complex with HEWL, is currently in progress and should allow us to understand the molecular basis of the ykfE-lysozyme interaction at atomic resolution. To denote its newly assigned function, ykfE has been registered under the new gene name Ivy (for inhibitor of vertebrate lysozyme) at the E. coli genetic stock center.

    EXPERIMENTAL PROCEDURES
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES

Cloning of ykfE-- The 474-base pair ykfE ORF including its own signal peptide was polymerase chain reaction amplified from E. coli K-12 MG1655 genomic DNA using pwo DNA polymerase (Roche Molecular Biochemicals). Primer sequences, 5'-TTATACCATGGGCAGGATAAGCTC-3' (sense) and 5'-GCTAAAGATCTAAAATTAAAGCCATCCGGA-3' (antisense) with NcoI (sense) and BglII (antisense) sites (underlined), were used. After digestion with NcoI + BglII, the polymerase chain reaction product was cloned into a pQE-60 vector (Qiagen) to express ykfE in phase with a C-terminal His6 tag (plasmid pQE-0220).

Expression and Purification of the YkfE Gene Product-- The ykfE gene product (Ivy) was expressed by culturing E. coli XL1-Blue carrying the plasmid pQE-0220 in LB + Amp medium. After initial growth at 37 °C, temperature was set at 30 °C when A600 reached 0.4, and Ivy expression was induced by adding 1 mM isopropyl-1-thio-beta -D-galactopyranoside. Cells were harvested at A600 around 2-2.5 and resuspended in Buffer A (20 mM sodium phosphate, pH 8.0, 300 mM NaCl) containing 1.5% Triton X-100, 1.5% glycerol, and 1 mg·ml-1 HEWL before sonication. Protein extraction was also performed in the absence of exogenous lysozyme to obtain lysozyme-free ykfE protein after the existence of a complex had been recognized. In both cases, purification was achieved by nickel affinity chromatography. The cleared lysate was applied to a 5-ml HiTrap chelating column (Amersham Pharmacia Biotech) charged with Ni2+ and was washed with 10 column volumes of Buffer A, followed by 10 column volumes of Buffer A containing 25 mM imidazole, and 5 column volumes of Buffer A containing 70 mM imidazole at a flow rate of 1 ml·min-1. Elution was performed with a linear gradient over 8 column volumes from 70 to 500 mM imidazole. The recombinant protein was eluted with 150-200 mM imidazole, and fractions were pooled and desalted against 20 mM Tris, pH 8.0, on a fast desalting column HR 10/10 (Amersham Pharmacia Biotech) at a flow rate of 5 ml·min-1. Protein concentration was determined by UV absorption at 280 nm using extinction coefficients calculated on the basis of tyrosine and tryptophan contents (8). Protein purity was assessed by SDS polyacrylamide gel electrophoresis and isoelectrofocusing (IEF) using 3 to 10 pH gradient pre-cast gels (Novex). Preliminary molecular weights for the purified proteins were estimated by gel filtration using a calibrated Superdex 75 HR10/30 column (Amersham Pharmacia Biotech) equilibrated with a 20 mM sodium citrate buffer, pH 6.5, at a flow rate of 0.5 ml·min-1. The purified proteins were characterized by mass spectroscopy (matrix-assisted laser desorption ionization/time of flight, Voyager DE-RP; PerSeptive Biosystems) and by N-terminal Edman sequencing (473A; Applied Biosystems).

Interaction Measurements-- To assay the interaction between Ivy and HEWL, 50 mg of HEWL were loaded on a nickel column at a flow rate of 1 ml·min-1 of 20 mM sodium phosphate, pH 8.0, 300 mM NaCl in the presence or absence of 3 mg of pure Ivy protein. After extensive washing with 20 mM sodium phosphate, pH 8.0, 1 M NaCl, elution was performed with a linear gradient over 5 column volumes to 1 M imidazole

Intrinsic protein fluorescence was measured with a Spex Fluorolog3 photon-counting spectrofluorimeter (Jobin Yvon-Spex, Longjumeau, France) equipped with a 450-watt Xenon source and a cooled photomultiplier. Tryptophan fluorescence emission spectra were recorded between 290 and 450 nm from solutions containing the individual proteins and from solutions containing a mixture of proteins excited with 280 nm of light. The degree of protein-protein interaction was determined from the extent of fluorescence quenching observed at 344 nm when spectra of a mixture of proteins were compared with the sum of the individual protein spectra at the same concentration. Interaction-dependent fluorescence quenching was determined in 10 mM Tris-HCl buffer, pH 7.0, 8.0, or 9.0, containing 100 mM NaCl at protein concentrations varying from 1 µM to 0.5 nM.

Determination of the Apparent Dissociation Constant (Ki)-- HEWL activity assay was performed at 25 °C in 100 mM potassium phosphate, pH 6.4, using 0.125 mg·ml-1 Micrococcus lysodeikticus (Sigma) as substrate. Inhibition studies were carried out by monitoring the change in turbidity associated with the lysis of M. lysodeikticus cells as described previously (9). One unit of HEWL activity was defined as the amount of enzyme causing a decrease in extinction of 0.001 per min at 450 nm. Ki value was determined according to the slow tight binding competitive inhibition model (with no conformational change) (10, 11). The following equation was used,
(V<SUB><UP>Ivy</UP></SUB>/V<SUB>0</SUB>)<SUP>2</SUP>+(V<SUB><UP>Ivy</UP></SUB>/V<SUB>0</SUB>)*(<UP>It/Et</UP>+K<SUB>i</SUB>/<UP>Et</UP>−1)−K<SUB>i</SUB>/<UP>Et</UP>=0 (Eq. 1)
where Ki is the apparent dissociation constant, Et is the total enzyme (HEWL) concentration, It is the total inhibitor (Ivy) concentration, VIvy is the inhibited velocity for a given concentration of Ivy, and V0 is the velocity in the absence of inhibitor.

HEWL (70 nM) was pre-incubated with Ivy (0-200 nM) at room temperature for 15 min prior to the addition of the M. lysodeikticus substrate (0.125 mg·ml-1). The Ki value was determined by fitting the experimental data onto the VIvy/V0 theoretical curves computed from the above equation (see Fig. 4).

Analysis of the Specificity of Ivy-- The effect of Ivy on C-type lysozyme activity was determined in the presence of 0.5 µg·ml-1 of HEWL (Sigma), with increasing concentrations of Ivy from 0 to 100 µg·ml-1. The effect on lambda  phage lysozyme activity was assayed in 20 mM Tris, pH 8.0, at 25 °C, according to Soumillion et al. (12) and using chloroform-treated E. coli K-12 MG1655 cells as substrate. Activity was determined by measuring the decrease of turbidity over time at 570 nm in the presence of 0.04 µg·ml-1 of lambda  phage lysozyme and concentrations of Ivy ranging from 0 to 6 µg·ml-1. The chitinase assay was performed in a 200 mM potassium phosphate buffer, pH 6.0, and 2 mM CaCl2 using crab shell chitin covalently linked with remazol brilliant violet 5R (Sigma) as substrate, according to Hackman and Golberg (13). The effect of Ivy on chitinase activity was determined in the presence of 0.5 µg·ml-1 of Streptomyces griseus chitinase (Fluka) at Ivy concentrations ranging from 0 to 5 µg·ml-1. The enzymatic activity was monitored at 575 nm.

Human saliva was also used as a source of lysozyme. 10 µl of fresh saliva were mixed with 1 ml of 100 mM potassium phosphate, pH 6.4, containing 0.125 mg·ml-1 M. lysodeikticus. Concentrations of Ivy ranging from 0 to 20 µg·ml-1 were used for this assay.

    RESULTS AND DISCUSSION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES

Exogenous HEWL is usually added prior to sonication to help the disruption of the E. coli cell wall according to the usual extraction protocol for recombinant proteins. HEWL is then removed during the subsequent purification steps. In the case of Ivy, a succession of anomalies led us to suspect a strong interaction between the two proteins. After the purification step by metal chelating chromatography on a nickel resin, SDS polyacrylamide gel electrophoresis analyses of the eluted proteins revealed the presence of two bands of nearly identical molecular mass, around 15 kDa, thus close to the predicted value for the mature form of Ivy (without signal peptide). Mass spectrometry and N-terminal sequencing clearly indicated that these fractions consisted of a mixture of two proteins present in equivalent quantities and identified one of them as the mature Ivy protein (molecular mass = 15.04 kDa) and the other as the exogenous HEWL (molecular mass = 14.3 kDa).

Preliminary results suggested the existence of a specific interaction between the two proteins. During metal chelating chromatography on a nickel resin, HEWL could only be retained if Ivy (extracted in the absence of lysozyme) had first been trapped on the column (see "Experimental Procedures"). The SDS polyacrylamide gel electrophoresis analysis of the eluted fractions confirmed the co-elution of Ivy and HEWL. Finally, the effect of the increase of HEWL concentrations on the IEF behavior of Ivy also suggested a strong interaction (Fig. 1). In the absence of HEWL, the IEF migration of Ivy exhibited two close bands at pI = 7.0 and pI = 6.7 (for a theoretical pI of 6.74). These two bands most likely correspond to the dimeric and monomeric forms of Ivy in solution. HEWL alone was found to migrate at pI>10. The increase of HEWL concentrations resulted in a decrease of intensity of the Ivy bands at pI = 7.0 and pI = 6.7 (Fig. 1) and the appearance of an extra band of material reverse migrating into the gel wells, at pI sime  10. 


View larger version (88K):
[in this window]
[in a new window]
 
Fig. 1.   Isoelectrofocusing analysis of pure Ivy complexed with various concentrations of HEWL.

The HEWL-Ivy interaction was further studied by fluorescence spectroscopy. The fluorescence spectrum of a 1 µM lysozyme, 1 µM Ivy mixture was found to differ significantly from that expected when adding the fluorescence emission spectra of the individual proteins. An overall 20% quenching of the fluorescence was measured with maximal quenching at 344 nm (Fig. 2). The shape and maximum of the spectrum are consistent with at least one relatively exposed tryptophan being quenched in the lysozyme-Ivy complex. The examination of the concentration dependence of the quenching spectrum showed that the shape of this spectrum was independent of the protein concentration between 1 nM and 1 µM. No reliable Kd value measurement could be obtained because of the insufficient intrinsic fluorescence intensity in the nM concentration range.


View larger version (28K):
[in this window]
[in a new window]
 
Fig. 2.   Intrinsic fluorescence quenching because of HEWL-Ivy interaction. The figure shows the fluorescence emission spectra of 300 nM HEWL (lower solid curve) and 300 nM Ivy (dashed curve) obtained separately. The dotted curve shows the experimental spectrum obtained for a 1:1 mixture of HEWL and Ivy, total protein concentration 600 nM. The upper solid curve is the expected emission spectrum for the mixture obtained by adding the spectra of the individual proteins. The difference between the upper solid and dotted curves (a quenching of ~20%) is attributed to the interaction between the two proteins. The spectra shown in this figure were obtained at pH 9.0. AU, arbitrary unit.

Finally, co-crystallization experiments and the subsequent analysis of the crystal content demonstrated the presence of both proteins, thus suggesting a specific and stable interaction between the two molecules (data not shown). The determination of the complex three-dimensional structure is currently in progress.

In addition to its specific physical interaction with HEWL, Ivy is also a potent inhibitor of HEWL enzymatic activity (Fig. 3). Preliminary experiments showed that in the presence of 1 µg·ml-1 of Ivy, the addition of 1 µg·ml-1 of HEWL produced a nonlinear kinetic with an upward concavity (Fig. 3a, curve b). In contrast, the pre-incubation of Ivy with HEWL for 15 min resulted in kinetic exhibiting a slight downward concavity (Fig. 3a, curve c). These results suggest a slow binding kinetic model for the Ivy-HEWL interaction. In addition, near-complete inhibition is reached for a range of Ivy concentrations comparable with the concentration of HEWL (see Figs. 3b and Fig. 4), indicating that Ivy behaves as a slow tight binding inhibitor. A Ki value of about 1 nM was thus estimated by fitting the experimental data (Fig. 4) with Morrison's equation corresponding to this model (see Eq. 1 and Refs. 10 and 11).


View larger version (14K):
[in this window]
[in a new window]
 
Fig. 3.   Progress curves of inhibition of HEWL by ykfE/Ivy. a, progress of hydrolysis of cell walls of M. lysodeikticus by 1 µg·ml-1 of HEWL (curve a) in the presence of 1 µg·ml-1 of Ivy without pre-incubation (curve b) or with 15-min. pre-incubation (curve c). The upward concavity of curve b corresponds to the latency in the inhibitory complex formation. Conversely, the slight downward concavity in curve c reflects a small dissociation (Ki approx  1 nM) of the inhibitory complex because of its initial dilution (70×) in the substrate mixture. b, progress of hydrolysis of cell walls of M. lysodeikticus by the addition of 1 µg·ml-1 of HEWL (curve a) to increasing concentrations of Ivy as follows: 1.0 (curve b); 1.2 (curve c); 1.6 (curve d), and 3.2 µg·ml-1 (curve e) without pre-incubation.


View larger version (10K):
[in this window]
[in a new window]
 
Fig. 4.   Effect of increasing concentrations of ykfE/Ivy on HEWL activity. The HEWL activity is plotted (black circles) for increasing Ivy concentrations. HEWL (70 nM) and Ivy (0 to 200 nM) were pre-incubated for 15 min before starting the reaction by adding M. lysodeikticus as substrate. Activities are expressed as a ratio between VIvy and V0, the initial velocities in the presence or absence of inhibitor, respectively. Ki was determined as the value allowing the best fit of the experimental data onto a slow competitive tight binding inhibition model described by Eq. 1 (see text). The curve corresponds to the model for a Ki value of 1 nM

The previous experiments demonstrated the potent inhibitory activity of Ivy on hen egg white lysozyme. We then explored the effect of Ivy on the related proteins of increasing evolutionary divergence. We selected a set of lysozyme and lysozyme-like proteins based on structural similarity using the MMDB data base (14). Using HEWL as initial query (MMDB accession number 1151), lambda  phage lysozyme (root mean square deviation, 1.3 Å; 21.1% identity), and chitinase (root mean square deviation, 1.9 Å; 11.1% identity) were selected as representatives of structural homologs with low sequence similarity. The inhibitory effect of Ivy was thus tested on the two proteins. Ivy was found to cause a weak inhibition of lambda  phage lysozyme (Fig. 5). The activity was only reduced by 15% at a molar ratio of 200:1, Ivy:lambda phage lysozyme. We found no inhibitory effect of Ivy on chitinase from S. griseus. We then investigated the capacity of Ivy to inhibit other C-type lysozymes and tested human saliva, because this secretion was reported to contain 30-55 µg·ml-1 of lysozyme (15). Ivy was found to strongly inhibit the lysozyme activity in saliva (Fig. 6). Around 50 µg·ml-1 of Ivy is sufficient to observe a decrease of 50% of the activity, which was fully abolished for an Ivy concentration of 0.5 mg per ml of saliva.


View larger version (11K):
[in this window]
[in a new window]
 
Fig. 5.   Comparative inhibition of HEWL (black circles) and lambda  phage lysozyme (open circles) activity by increasing concentrations of ykfE/Ivy.


View larger version (9K):
[in this window]
[in a new window]
 
Fig. 6.   Inhibition of lysozyme activity of human saliva by increasing concentrations of ykfE/Ivy.

On a gel filtration column, Ivy is eluted with an apparent molecular mass of about 30 kDa, indicating that the predominant form in solution is a homodimer, as already suggested by IEF experiments. Fluorescence studies confirmed this model. The fluorescence emission spectrum of HEWL exhibits a broad peak with a maximum at 342 nm and a long wavelength tail typical of relatively exposed tryptophan residues. In contrast, the spectrum of Ivy shows a peak at 334 nm ~25% more intense on an absolute scale and 2.5 times more intense on a per tryptophan scale (Fig. 2). Such intense fluorescence and the relatively short wavelength of maximum emission both argue for tryptophans buried within apolar environments. Furthermore, the shape of the emission spectrum was found to be independent of the protein concentration in a broad 0.5 nM to 1 µM range and appears insensitive to change in pH between 7.0 and 9.0. The order of magnitude of the dimerization Kd appeared much lower than 10-9 M, although no precise measurement could be made in this concentration range. Altogether, these biophysical results suggest that the Ivy homodimer is the physiologically active unit.

C-type lysozyme is an ancient protein whose origin goes back about 500 million years (16). It has long been recognized that lysozymes (the family of enzymes hydrolyzing the 1,4-beta linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in the peptidoglycan moiety of bacterial cell walls) are part of a nonimmunological ancestral bactericidal system in vertebrates. C-type lysozyme is found in the serum (17-19), in milk (20, 21), in the digestive tract (22), in the airway (23), and in all mucosal surfaces and secretions (24-31). There is multiple evidence that lysozymes play a significant role in the control of the host microflora to prevent infection (32-36). Bacterial C-type lysozyme inhibitors might thus have emerged to balance the host defense. Indeed, an increase of anti-lysozyme activity has been linked to bacterial persistence in several systems (37, 38). However, lysozyme inhibitors could also be directed against lysozyme activities of other microorganisms and play a role in ecological competition (39, 40). Finally, these inhibitors could also have emerged as a protection against bacteriophage-encoded lysozymes, the activity of which is essential to the release of mature virions (41). It thus makes evolutionary sense that bacteria might have evolved a resistance mechanism against the bactericidal activity of various lysozymes found in their environment. However, it must be noted that for Gram-negative bacteria such as E. coli, the presence of an outer membrane impermeable to molecules larger than 0.6 kDa should be sufficient to protect the peptidoglycan moiety from the lysozymes present in the medium.

We selected ykfE as an ORFan gene expressed by E. coli K12 (5). The presence of a signal peptide predicted a periplasmic location for its protein product, which is now consistent with its newly assigned function. Our biochemical and functional analyses of Ivy show that its predominant homodimeric form strongly interacts with hen and human, and probably all C-type lysozymes, thereby abrogating their activity in a stoichiometric manner. Ivy does inhibit C-type lysozymes under physiological conditions, as tested in human saliva, the secretion where lysozyme is naturally found at the highest concentration. It is thus likely that at least one purpose of Ivy is to protect E. coli from its natural host lysozyme bactericidal activity, for instance in cases where the integrity of the outer membrane might be compromised (e.g. by chemically aggressive compounds in the medium or at the time of cell division).

As such a resistance mechanism against an ubiquitous bactericidal enzyme should be advantageous to all murein-containing bacteria, in particular Gram-positive bacteria, ykfE/Ivy-like genes are expected to exist in many bacterial genomes, making its ORFan nature a paradox. Indeed, we detected a putative ortholog of E. coli Ivy within the recently published genome of Pseudomonas aeruginosa (1). However, the two protein sequences only share 30% of identical residues in their most similar region, indicating a fast divergence rate (Fig. 7). It is thus likely that genes of the ykfE/Ivy family are not detected in other bacteria because of their low sequence conservation. It is our hope that the knowledge of the three-dimensional structure of Ivy will allow the discovery of other Ivy homologues by the identification of a set of critical positions in the sequence beyond the twilight zone of sequence similarity.


View larger version (29K):
[in this window]
[in a new window]
 
Fig. 7.   Amino acid sequence alignment of ykfE/Ivy versus P. aeruginosa ORF PA3902. The depicted alignment has been produced using default parameters in FASTA (42). The underlined sequence corresponds to the known signal peptide in Ivy.


    ACKNOWLEDGEMENTS

We thank Dr. C. Cambillau for access to x-ray diffraction equipment and helpful discussions and Dr. Mary Berlin for quick validation of the Ivy name. We also acknowledge the helpful comments of anonymous referees concerning the analysis of the Ivy inhibition mechanism. We thank Dr. C. Evrard for the gift of lambda  phage lysozyme.

    FOOTNOTES

* The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

§ To whom correspondence should be addressed. Tel.: 33 04 91 16 45 48; Fax: 33 04 91 16 45 49; E-mail: vincent.monchois@igs.cnrs-mrs.fr.

Published, JBC Papers in Press, February 23, 2001, DOI 10.1074/jbc.M010297200

    ABBREVIATIONS

The abbreviations used are: ORF(s), open reading frame(s); HEWL, hen egg white lysozyme; IEF, isoelectrofocusing.

    REFERENCES
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES

1. Stover, C. K., Pham, X. Q., Erwin, A. L., Mizoguchi, S. D., Warrener, P., Hickey, M. J., Brinkman, F. S., Hufnagle, W. O., Kowalik, D. J., Lagrou, M., Garber, R. L., Goltry, L., Tolentino, E., Westbrock-Wadman, S., Yuan, Y., Brody, L. L., Coulter, S. N., Folger, K. R., Kas, A., Larbig, K., Lim, R., Smith, K., Spencer, D., Wong, G. K., Wu, Z., and Paulsen, I. T. (2000) Nature 406, 959-964[CrossRef][Medline] [Order article via Infotrieve]
2. Fischer, D., and Eisenberg, D. (1999) Bioinformatics 15, 759-762[Free Full Text]
3. Alimi, J. P., Poirot, O., Lopez, F., and Claverie, J. M. (2000) Genome Res. 10, 959-966[Abstract/Free Full Text]
4. Blattner, F. R., Plunkett, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., et al.. (1997) Science 277, 1453-1474[Abstract/Free Full Text]
5. Wasinger, V. C., and Humphery-Smith, I. (1998) FEMS Microbiol. Lett. 169, 375-382[CrossRef][Medline] [Order article via Infotrieve]
6. Pasquali, C., Frutiger, S., Wilkins, M. R., Hughes, G. J., Appel, R. D., Bairoch, A., Schaller, D., Sanchez, J. C., and Hochstrasser, D. F. (1996) Electrophoresis 17, 547-555[Medline] [Order article via Infotrieve]
7. Abergel, C., Monchois, V., Chenivesse, S., Jeudy, S., and Claverie, J. M. (2000) Acta Crystallogr. 56, 1694-1695
8. Gill, S. C., and von Hippel, P. H. (1989) Anal. Biochem. 182, 319-326[Medline] [Order article via Infotrieve]
9. Charlemagne, D., and Jollès, P. (1970) C. R. Acad. Sci. (Paris) 2721-2723
10. Morrison, J. F. (1969) Biochim. Biophys. Acta 185, 269-286[Medline] [Order article via Infotrieve]
11. Morrison, J. F., and Walsh, C. (1988) Adv. Enzymol. Relat. Areas Mol. Biol. 61, 201-301[Medline] [Order article via Infotrieve]
12. Soumillion, P., Jespers, L., Vervoors, J., and Fastrez, J. (1995) Protein Eng. 8, 451-456[Abstract]
13. Hackman, R. H., and Golberg, M. (1964) Anal. Biochem. 8, 397-401
14. Wang, Y., Addess, K. J., Geer, L., Madej, T., Marchler-Bauer, A., Zimmerman, D., and Bryant, S. H. (2000) Nucleic Acids Res. 28, 243-245[Abstract/Free Full Text]
15. Taylor, D. C., Cripps, A. W., and Clancy, R. L. (1992) J. Immunol. Methods 146, 55-61[Medline] [Order article via Infotrieve]
16. Qasba, P. K., and Kumar, S. (1997) Crit. Rev. Biochem. Mol. Biol. 32, 255-306[Abstract]
17. Wilson, K. P., Malcom, B. A., and Matthews, B. W. (1992) J. Biol. Chem. 267, 10842-10849[Abstract/Free Full Text]
18. Gemsa, D., Davis, S. D., and Wedgwood, R. J. (1996) Nature 210, 950-951
19. Selsted, M. E., and Martinez, R. J. (1978) Infect. Immun. 20, 782-791[Medline] [Order article via Infotrieve]
20. Murakami, K., Lagarde, M., and Yuki, Y. (1998) Electrophoresis 19, 2521-2527[Medline] [Order article via Infotrieve]
21. Hamosh, M. (1998) Biol. Neonate 74, 163-176[CrossRef][Medline] [Order article via Infotrieve]
22. Peeters, T., and Vantrappen, G. (1975) Gut 16, 553-558[Abstract]
23. Jacquot, J., Hayem, A., and Galabert, C. (1992) Eur. Respir. J. 5, 343-358[Abstract]
24. Lim, D. J., Liu, Y. S., and Birck, H. (1976) Ann. Otol. Rhinol. Laryngol. 85, 50-60[Medline] [Order article via Infotrieve]
25. McNabb, P. C., and Tomasi, T. B. (1981) Annu. Rev. Microbiol. 35, 477-496[CrossRef][Medline] [Order article via Infotrieve]
26. Cohen, M. S., Black, J. R., Proctor, R. A., and Sparling, P. F. (1984) Scand. J. Urol. Nephrol. Suppl. 86, 13-22[Medline] [Order article via Infotrieve]
27. Tachibana, M., Morioka, H., Machino, M., and Mizukoshi, O. (1986) Auris Nasus Larynx 13, 97-99[Medline] [Order article via Infotrieve]
28. Hanamure, Y., and Lim, D. J. (1986) Am. J. Otolaryngol. 7, 410-425[Medline] [Order article via Infotrieve]
29. McClellan, K. A. (1997) Surv. Ophthalmol. 42, 233-246[CrossRef][Medline] [Order article via Infotrieve]
30. Schenkels, L. C., Veerman, E. C., and Nieuw Amerongen, A. V. (1995) Crit. Rev. Oral Biol. Med. 6, 161-175[Abstract]
31. Cole, A. M., Dewan, P., and Ganz, T. (1999) Infect. Immun. 67, 3267-3275[Abstract/Free Full Text]
32. Kondo, L. R., Hanna, L., and Keshishyan, H. (1973) Proc. Soc. Exp. Biol. Med. 142, 131-132
33. Walker, W. A. (1979) Ciba Found. Symp. 70, 201-219[Medline] [Order article via Infotrieve]
34. Ved'mina, E. A., Pasternak, N. A., Shenderovich, V. A., Zhuravleva, T. P., and Andrusenko, I. T. (1979) Antibiot. Khimioter. 24, 746-750
35. Hancock, R. E., and Scott, M. G. (2000) Proc. Natl. Acad. Sci. U. S. A. 97, 8856-8861[Abstract/Free Full Text]
36. Vollmer, W., and Tomasz, A. (2000) J. Biol. Chem. 275, 20496-20501[Abstract/Free Full Text]
37. Bukharin, O. V. (1994) Zh. Mikrobiol. Epidemiol. Immunobiol. 1, (Suppl.), 4-13
38. Bondarenko, V. M., Petrovskaia, V. G., and Iablochkov, A. L. (1994) Zh. Mikrobiol. Epidemiol. Immunobiol. 1, (Suppl.), 22-28
39. Nemtseva, N. V. (1997) Zh. Mikrobiol. Epidemiol. Immunobiol. 4, 123-126[Medline] [Order article via Infotrieve]
40. Lentsner, A. A., Lentsner, Kh. P., and Toom, M. A. (1975) Zh. Mikrobiol. Epidemiol. Immunobiol. 8, 77-81[Medline] [Order article via Infotrieve]
41. Bukharin, O. V., and Deriabin, D. G. (1989) Zh. Mikrobiol. Epidemiol. Immunobiol. 11, 16-19[Medline] [Order article via Infotrieve]
42. Pearson, W. R. (2000) Methods Mol. Biol. 132, 185-219[Medline] [Order article via Infotrieve]


Copyright © 2001 by The American Society for Biochemistry and Molecular Biology, Inc.