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Journal of Bacteriology, August 2006, p. 6020-6025, Vol. 188, No. 16
0021-9193/06/$08.00+0 doi:10.1128/JB.00379-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Peptidyl-Prolyl cis/trans Isomerase-Independent Functional NifH Mutant of Azotobacter vinelandii
Nara Gavini,*
Sudheer Tungtur, and
Lakshmi Pulakat
Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762
Received 16 March 2006/
Accepted 25 May 2006

ABSTRACT
Peptidyl-prolyl
cis/trans isomerases (PPIases) play a pivotal
role in catalyzing the correct folding of many prokaryotic and
eukaryotic proteins that are implicated in a variety of biological
functions, ranging from cell cycle regulation to bacterial infection.
The
nif accessory protein NifM, which is essential for the biogenesis
of a functional NifH component of nitrogenase, is a PPIase.
To understand the nature of the molecular signature that defines
the NifM dependence of NifH, we screened a library of
nifH mutants
in the nitrogen-fixing bacterium
Azotobacter vinelandii for
mutants that acquired NifM independence. Here, we report that
NifH can acquire NifM independence when the conserved Pro258
located in the C-terminal region of NifH, which wraps around
the other subunit in the NifH dimer, is replaced by serine.

TEXT
Peptidyl-prolyl
cis/trans isomerases (PPIases) catalyze the
cis/
trans isomerization of the peptidyl-prolyl peptide bond
in oligopeptides and proteins, a rate-limiting step in the process
of protein folding that is essential for generating functional
proteins (
5-
7). Some denatured proteins regain their native
conformations within milliseconds to seconds, whereas others
refold very slowly, with the time ranging from minutes to hours.
The slow conformational changes arise from the well-known delocalization
of electrons in the amide bond and are even more pronounced
if additional steric constraints are imposed by the proline
ring. PPIases enhance the rate of refolding of the slowly folding
forms of denatured proteins by catalyzing the
cis/
trans isomerization
of these peptidyl-prolyl bonds (
5,
19). PPIases are regulators
of a variety of biological functions, such as cell cycle progression
(Pin1 and ESS1) (
4,
10,
16), the inhibition of apoptosis (cyclophilins
A) (
17), carcinogenesis (Pin1) (
2), association with hormone
receptors (FKBP52/CyP40) (
24), and bacterial infection (MIP)
(
14,
21), to name a few. The PPIase family consists of three
subfamilies, the cyclophilins, the FK506 binding proteins, and
the parvulins. Recently, based on homology analysis and activities,
we proposed that the
nif accessory protein NifM is also a PPIase
and that it belongs to the family of parvulins (
8,
18,
26).
Nitrogenase, the key enzyme that catalyzes biological nitrogen fixation, requires several accessory proteins for the maturation and assembly of its components, the MoFe-protein and NifH (3, 25). A major breakthrough in understanding the structural properties of nitrogenase came with the availability of the crystallographic structures of its component proteins (9, 22, 23, 27). The cloning and sequencing of most of the genes involved in the synthesis and assembly of nitrogenase, in turn, has given us an elegant picture of its genetic complexity (12). NifH, the obligate electron donor to the MoFe protein, has multiple roles in the catalytic process of biological nitrogen fixation, as well as in the maturation and assembly of nitrogenase (1, 3, 11, 20, 31). These include involvement in the initial biosynthesis of FeMo cofactor and in the insertion of preformed FeMo cofactor into an inactive FeMo cofactor-deficient MoFe protein. The synthesis of a functional NifH is dependent on the availability of a nif accessory protein, NifM (11). An examination of the consensus peptide sequence of NifH derived by comparing 60 different sequences shows the existence of seven fully conserved proline residues (Fig. 1). Therefore, it is reasonable to assume that the stability and activity of NifH largely depend upon the appropriate conformation of the peptidyl-prolyl bonds present in this protein.
The
nifM Azotobacter vinelandii strain, designated BG98, generated
by inserting a kanamycin resistance (
kan) gene into
nifM, was
used for this purpose. This strain was constructed using the
same strategy that we had used for generating the
nifM A. vinelandii strain that carried a
lacZ-kan gene cassette (
15). It showed
a Nif
phenotype, since in the absence of functional NifM,
NifH is nonfunctional, and it could not grow on Burke's nitrogen-free
medium (BN
). To obtain enriched
A. vinelandii NifM, we
generated a His-tagged NifM translational fusion under the transcriptional
control of the
nifH promoter in the broad-host-range plasmid
pBG2401 (Fig.
2a). From this construct, NifM was expressed as
a His-tagged fusion protein with the His tag at the N terminus.
The
nifM A. vinelandii BG98 was transformed with pBG2401, and
the transformants were selected on BN
Kan agar plates.
These transformants could grow on BN
Kan agar plates,
suggesting that the His-tagged NifM (from pBG2401) was functional
and could confer a Nif
+ phenotype on
A. vinelandii BG98. Overexpression
of the NifM protein was achieved by incubating the cells for
5 hours in BN
medium and activating the strong
nifH promoter.
The overexpressed NifM from
A. vinelandii BG98 was partially
purified using nickel columns (Fig.
2b). The PPIase activity
of this NifM was measured by using the standard protease-coupled
assay (
5,
19,
25). The chromogenic substrate used was succinyl-Ala-Phe-Pro-Phe-4-nitroanilide.
The substrate was dissolved in 460 mM LiCl in trifluoroethanol
as described previously (
19) to increase the concentration of
the
cis isomer. The assay was performed at 10°C as described
previously (
5,
19,
25) using different amounts of enriched NifM
and substrate for a range of time periods. Addition of NifM
to the oligopeptide substrate enhanced the conversion of the
cis isomers to
trans isomers. The appearance of nitroanilide
(resulting from the cleavage of the
trans isomer of succinyl-Ala-Phe-Pro-Phe-4-nitroanilide
by chymotrypsin) was measured by monitoring the absorbance at
390 nm spectrophotometrically. The control sample contained
crude extracts of
A. vinelandii BG98, which is devoid of functional
NifM. It was found that
A. vinelandii NifM demonstrated PPIase
activity with a specificity constant of 1.09
x 10
7/M/s. This
value is comparable to the reported specificity constant of
the
Escherichia coli PPIase, PPiC (parvulin; EC 5.2.1.8), which
is 1.69
x 10
7/M/s when succinyl-Ala-Leu-Pro-Phe-4-nitroanilide
is used as a substrate (
19). These results suggested that the
extent of PPIase activity that NifM exhibited was comparable
to that of
E. coli PpiC, which shares homology with NifM.
Since NifM is a PPIase and it interacts with NifH, the possible
substrate for NifM can be any of the conserved proline residues
present in NifH. Therefore, it is conceivable that NifM-independent
nifH genetic mutants can be isolated. We utilized a DNA-shuffling
technique (
13,
29) to generate a large number of
nifH mutants
and analyzed whether any of the mutants attained NifM independence.
This library of
nifH mutants was initially screened for the
Nif
+ phenotype by testing their abilities to grow on agar plates
with BN
(
30). Then, the abilities of the NifH proteins
encoded by these mutants to function independently of NifM were
tested. To do this, the
nifH genes of these mutants were PCR
amplified using the specific
nifH primers, and the resulting
PCR products were individually ligated into pCR2.1TOPO vector
(Invitrogen Corp., Carlsbad, CA). The cloned mutant
nifH genes
were subjected to nucleotide sequence analysis. Details of the
mutations in these
nifH mutants are described elsewhere (unpublished
data). The plasmids containing mutant
nifH genes with amino
acid changes were then transformed into the
nifM A. vinelandii BG98. The transformants were tested for the ability to grow
on BN
Kan agar plates. Since the pCR2.1TOPO vector has
a pUC
ori, it cannot replicate in
A. vinelandii. However, if
the mutant
nifH could confer a Nif
+ phenotype in the absence
of NifM, it would be rescued onto the chromosome via homologous
recombination. Therefore, the
nifM A. vinelandii BG98 transformants
that could grow on BN
Kan plates carry a mutant
nifH that is capable of participating in nitrogen fixation without
the help of NifM. We found that one of the
nifH mutants had
two amino acid changes, P232K (CCG

AAG) and P258S (CCG

TCG), and
was able to impart to the
nifM A. vinelandii BG98 strain the
ability to grow on BN
Kan plates. This
nifH mutant was
present in the original clone, designated pBG1528. The
nifM A. vinelandii BG98 that rescued this
nifH mutant onto the chromosome
was designated
A. vinelandii BG1528. Comparison of the growth
of this strain in BN
liquid medium to that of the wild-type
A. vinelandii is shown in Fig.
3a. Since both amino acid replacements
in this mutant were conserved proline residues and the NifH
encoded by this mutant could function independently of NifM,
we hypothesized that these proline residues might serve as the
substrates for the PPIase activity of NifM. We analyzed which
of these replacements was absolutely essential for achieving
NifM independence of NifH. One of the DNA-shuffling mutants
carried only the P232K amino acid replacement. To generate a
nifH mutant that carried only the P258S amino acid replacement,
we utilized the conveniently located site for the restriction
enzyme SalI in the
nifH coding sequence (Fig.
3b). We separated
the DNA fragments carrying the mutations by digesting them with
SalI and joining the wild-type
nifH fragment with the mutant
nifH fragment carrying a CCG

TCG mutation at position C775. Figure
3b shows the resulting
nifH plasmids and the Nif phenotypes
they imparted to the
nifM A. vinelandii BG98. These plasmids
are derivatives of pBHR1 (a broad-host-range vector from MobBiTec,
Germany) and replicate in
A. vinelandii. nifM A. vinelandii BG98 was transformed using these plasmids, and the Nif phenotypes
of the resulting transformants were analyzed by observing their
growth on BN
plates (Fig.
4a) and also in BN
liquid
medium (Fig.
3a). It was found that the P258S amino acid change
(pBG3605) imparted a Nif
+ phenotype to the
nifM A. vinelandii BG98. The P232K amino acid change (pBG3609) was unable to do
so. This result implied that the region of NifH spanning P258
serves as the substrate for the NifM protein and that the region
spanning P232 is not involved in this function. According to
the structure of NifH (Protein Data Bank code 2NIP) (
9,
28),
P258 is located in the C-terminal region of NifH, which wraps
around the other subunit of the NifH dimer (Fig.
4b). It is
conceivable that the
trans conformation of the peptidyl-prolyl
bond of P258 contributes significantly to the structure of this
region and that NifM-mediated modification is essential to attain
this structure.
Our results suggest that the NifM-mediated conversion to the
trans conformation of the peptidyl-prolyl bond of Pro258 is
crucial for the proper folding, maturation, and assembly of
the functional NifH dimer. We also show that altering this molecular
signature of NifM dependence by replacing P258 with serine is
sufficient to generate a NifM-independent NifH. Thus, our results
delineate the specific site on NifH where NifM exerts its effect
as a molecular chaperon of NifH and demonstrate an alternative,
chaperon-independent mechanism by which the functional conformation
can be achieved. More importantly, the P258S mutant
nifH is
the first example of a PPIase-independent functional mutant.
Our approach has allowed us to differentiate a proline-peptide
bond (P258) in NifH that serves as a substrate for the PPIase
activity of NifM from one that does not (P232). The PPIases
are ubiquitous and influence several fundamental biological
functions, including cell division and oncogenesis. Therefore,
a method to identify their site of action in a given substrate,
similar to the approach used here, can be utilized to delineate
PPIase-mediated influences.

ACKNOWLEDGMENTS
This research was supported by the NSF (N.G. and L.P.).
We thank members of the Gavini-Pulakat laboratory for helpful discussions and technical help.

FOOTNOTES
* Corresponding author. Mailing address: Department of Biological Sciences, P.O. Box GY, Mississippi State University, Mississippi State, MS 39762. Phone: (662) 325-7573. Fax: (662) 325-7939. E-mail:
gavini{at}biology.msstate.edu.

Dedicated to the memory of the late Barbara K. Burgess, of the University of California at Irvine, who strove to improve the lives of foreign and female students. 

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Journal of Bacteriology, August 2006, p. 6020-6025, Vol. 188, No. 16
0021-9193/06/$08.00+0 doi:10.1128/JB.00379-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
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