downloaded from //jb.asm.org/content/jb/early/2010/01/29/jb.01471... · fha and kinase domain sites...
TRANSCRIPT
1
Archaeal eukaryote-like serine/threonine protein kinase interacts 1
with and phosphorylates a forkhead-associated domain-containing 2
protein 3
Bin Wang, Shifan Yang, Lei Zhang, Zheng-Guo He* 4
National Key Laboratory of Agricultural Microbiology, Center for Proteomics 5
Research, College of Life Science and Technology, Huazhong Agricultural 6
University, Wuhan 430070, China. 7
Running title: Archaeal kinase phosphorylates FHA protein 8
*To whom correspondence should be addressed: 9
College of Life Science and Technology, Huazhong Agricultural University, Wuhan 10
430070, China 11
Email: [email protected] or [email protected] 12
Tel: +86-27-87284300, Fax: +86-27-87280670 13
Key words: Ser/Thr protein kinase; FHA domain; Archaea; Phosphorylation 14
Conflict of interest: The authors declare that they have no conflict of interest. 15
16
Copyright © 2010, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.J. Bacteriol. doi:10.1128/JB.01471-09 JB Accepts, published online ahead of print on 29 January 2010
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
2
ABSTRACT 1
Protein phosphorylation plays an important role in cell signaling. However, in 2
the Archaea, little is known regarding which proteins are phosphorylated and which 3
kinases are involved. In this study, we have identified, for the first time, a typical 4
eukaryote-like Ser/Thr protein kinase and its protein partner, a forkhead-associated 5
(FHA) domain-containing protein, from the archaeon Sulfolobus tokodaii str.7. The 6
protein kinase, ST1565, physically interacted with the FHA domain protein, ST0829, 7
both in vivo and in vitro. ST1565 preferred Mn2+
as its cofactor for 8
auto-phosphorylation and for substrate-phosphorylation, at an optimal temperature 9
45°C and optimal of pH 5.5-7.5. The critical amino acid residues in the conserved 10
FHA and kinase domain sites were identified through a series of mutation assays. 11
Threonine-329 was part of a major activation site in the kinase, while Threonine-326 12
was a negative regulation site. Several amino acid substitution mutants in the 13
conserved FHA domain sites of ST0829 lost their physical interactions with ST1565. 14
A structure model for the FHA domain demonstrated that these mutation sites were 15
located at the edge of the protein, and thus, constituted the potential interaction 16
domain with ST1565. This report presents pioneering work on the third domain of the 17
Archaea, showing that a protein kinase interacts with and phosphorylates its FHA 18
domain protein. These data provide critical information on the structural or functional 19
characteristics of archaeal proteins and can help to accelerate the understanding of 20
fundamental signaling mechanisms in all three domains of life forms. 21
22
23
24
25
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
3
INTRODUCTION 1
Protein phosphorylation is most commonly exploited by cells to allow appropriate 2
responses to various environmental cues (9). Long considered to be restricted to the 3
Eucarya, homologues of eucaryal protein kinases have since been reported in 4
Bacteria and more recently in Archaea (10). The importance of Ser/Thr/Tyr kinases in 5
cell signaling in eukaryotes has been widely documented (20, 22). Protein 6
phosphorylation has been less intensively studied in archaea, a so-called “the third 7
domain” life, whose members usually live in extreme environments, such as those 8
with high salt content, high temperature, or extreme pH. 9
The first evidence for Ser/Thr/Tyr protein phosphorylation in Archaea was 10
reported in the extreme halophilic Halobacterium salinarum following 32
P 11
radiolabeling (29). Subsequently, protein phosphorylation of an isolated ribosomal 12
fraction from the extreme acidothermophilic archaeon, Sulfolobus acidocaldarius, 13
was characterized (26, 27). Several studies have also employed phosphoamino 14
acid-directed antibodies to provide direct evidence for the presence of 15
phosphotyrosine in archaeal proteins from Sulfolobus solfataricus, Haloferax volcanii, 16
and Methanosarcina thermophila TM-1 (1). Based on a comprehensive analysis of 17
completed genome sequences, archaeal representatives of novel putative protein 18
kinase families have been reported (17). Several kinase activities have since been 19
confirmed (18, 19). Furthermore, the recent elucidation of the crystal structure of the 20
archaeon Archaeoglobus fulgidus Rio2 now suggests that this protein defines an 21
entirely new family of protein kinases (12-15). 22
In the Archaea, the actual proteins that are phosphorylated and which kinases are 23
involved in the reaction remain largely unknown (32). Among the archaeal proteins, 24
the CheA and CheY from Halobacterium salinarum are two of the best characterized 25
sensor and response regulator proteins associated with phosphorylation (6, 31). A 26
two-component system has been proposed for responses to various chemotactic and 27
photactic stimuli in the Archaea (23, 24). Recently, Aivaliotis et al have completed a 28
genome-wide and site-specific phosphoproteome analysis of H. salinarum. They 29
indicate that phosphoproteins are involved in a wide variety of cellular processes, and 30
are especially enriched in metabolic and translation processes (1). Their study offers 31
systematic evidence that protein phosphorylation is a general and fundamental 32
regulatory process that is not restricted to eukaryotes and bacteria. Sequence evidence 33
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
4
suggests that archaeons contain abundant protein kinases that are themselves 1
phosphorylated on serine, threonine, and tyrosine residues. 2
Some archaeal open reading frames (ORFs) exhibit a number of the characteristic 3
features of the eukaryotic protein kinase superfamily (1, 25). However, overall level 4
of sequence identity is not particularly high in these deduced protein kinases. 5
Although catalytic capabilities have been inferred from their primary sequence, the 6
structural or functional properties of archaeal protein kinases have not been 7
characterized. For example, although the importance of Ser/Thr/Tyr kinases for cell 8
signaling has been widely documented in eukaryotes and in some bacteria, very few 9
target substrates for archaeal protein kinases have been identified. 10
Recently, a protein containing a forkhead-associated (FHA) domain has been 11
proposed to interact with a protein partner in a process regulated by reversible protein 12
phosphorylation (4). The FHA domain was determined to be a phosphoprotein 13
recognition unit, with a preference for phospho-threonine (pT) peptides (4, 5, 33). It 14
usually exists in eukaryotic proteins, for example in several forkhead-type 15
transcription factors (8), and has been characterized in some bacterial proteins (21). 16
These domains bind phospho-threonine peptides and mediate 17
phosphorylation-dependent protein-protein interactions in a variety of cell signaling 18
processes (21). However, the residues within this FHA domain are not well 19
conserved, although there do appear to be conserved residues that are involved in 20
recognition of the phosphopeptide backbone or pT residue (4, 5). There have been no 21
reports as yet of any binding partner for any archaeal FHA domain (21). 22
In this study, we have identified a typical eukaryote-like Ser/Thr protein kinase 23
and its protein partner, an FHA domain-containing protein, from the archaeon S. 24
tokodaii str.7. The protein kinase, ST1565, physically interacts with the FHA domain 25
protein, ST0829, both in vivo and in vitro. ST1565 has clear auto-phosphorylation and 26
substrate-phosphorylation activities. Conserved FHA and kinase domain sites have 27
been further identified through a series of mutation assays. This report demonstrates, 28
for the first time, a protein kinase interacting with and phosphorylating its FHA 29
domain protein, respectively, in the third domain of Archaea. Our findings present 30
essential information on the structural or functional characteristics of aforementioned 31
archaeal proteins. 32
33
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
5
MATERIALS AND METHODS 1
Strains, enzymes, plasmids, and reagents 2
Escherichia coli BL21 (F-ompT hsdSB(rB
-mB
-) gal
-dcm (DE3)) cells and pET28a 3
containing the T7 RNA polymerase promoter were purchased from Novagen, and were used 4
to express archaeal proteins. pBT, pTRG vectors, E. coli XR host strains, and the reagents for 5
two-hybrid assay were purchased from Stratagene. Restriction enzymes, T4 ligase, DNA 6
polymerase, dNTPs and all antibiotics were obtained from TaKaRa Biotech. PCR primers 7
were synthesized by Invitrogen (Supplemental Table S1). Ni-NTA (Ni2+
-nitrilotriacetate) and 8
GST agarose were obtained from Qiagen. 9
Cloning and purification of archaeal proteins 10
Prokaryotic recombinant vectors expressing the genes for archaeal proteins and their 11
mutant proteins were constructed. E. coli BL21 CodonPlus (DE3)-RIL cells (Novagen) were 12
used as the host strain to express archaeal proteins as described (34). Protein concentrations 13
were determined by spectrophotometric absorbance at 260 nm, according to Gill and Hippel 14
(7). 15
Bacterial two-hybrid analysis 16
BacterioMatch II Two-Hybrid System Library Construction Kit (Stratagene) was used to 17
detect protein-protein interactions between protein kinase and FHA protein. The bacterial 18
two-hybrid system detects protein-protein interactions based on transcriptional activation and 19
the analysis was carried out according to the procedure supplied with the commercial kit and 20
our previously published procedures (34). The archaeal genes were amplified by PCR 21
using their specific primer pairs (Supplemental Table S1) from genomic DNA of S. 22
tokodaii. pBT and pTRG vectors containing archaeal genes of protein kinase and FHA 23
protein were generated. Positive-growth co-transformants were selected on the Screening 24
Medium plate containing 5 mM 3-AT (Stratagene), 8 µg/ml streptomycin, 15 µg/ml 25
tetracycline, 34 µg/ml chloramphenicol, and 50 µg/ml kanamycin. 26
GST pull-down assay 27
Equimolar amounts of normalized GST or GST-ST0829 proteins were combined with 28
equimolar amounts of normalized his-tagged-ST1565 proteins in 1.5 mL tubes containing 500 29
µL of PBS. The protein mixture was gently rocked at 4°C for 4-15 h. Before further 30
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
6
purification, 60 µL of mixture was removed and saved as a loading control. The remaining 1
mixtures were then purified using the GST-affinity assay as described above. All samples 2
were subjected to SDS-PAGE. The protein bands were transferred to a nitrocellulose 3
membrane. Western blot analysis was conducted using primary anti-ST1565 antibody 4
(1:1000) and secondary antibody IgG-HRP (goat anti-Rabbit) (1:10000). To quantify the 5
protein, the signal was developed using DAB detection reagents, and it was photographed to 6
serve as a record. 7
Co-IP Assays 8
The in vivo interactions between protein kinase and FHA protein were analyzed by Co-IP 9
according to our modified previously published procedures (34). Exponentially growing cells 10
of S. tokodaii were harvested, resuspended, and lysed in 4 mL of buffer [50 mM Tris-HCl (pH 11
7.5), 150 mM NaCl, 1 mM EDTA, 0.5% Nonidet P-40]. Co-IPs were performed by 12
incubating and shaking 10 µg of archaeal cell extract with 3 µL of ST0829 antiserum in 100 13
µL of buffer for 3 h at 4 °C. A 20-µL slurry of protein A Sepharose was added, and incubation 14
was continued for another hour. Immune complexes were collected, and the beads were 15
washed with buffer. Finally, the beads were resuspended in SDS/PAGE sample buffer. After 16
boiling, the samples were analyzed by Western blotting using anti-ST1565 antibody. 17
Assay of protein kinase activity 18
Protein kinase activity was routinely assayed in the solution. Briefly, in vitro 19
phosphorylation was carried out by incubating 0.25 nM S. tokodaii protein kinase and 2.5 nM 20
FHA domain protein in buffer (20 mM Hepes [pH 7.4], 10 mM MgCl2, and 10 mM MnCl2) 21
containing 300 µCi [γ-32
P]ATP for 30 min at 55 °C. The reaction was stopped with excess 22
sample buffer, and proteins were separated on 10% SDS-PAGE and analyzed by 23
autoradiography. Mg2+
, Mn2+
, and divalent cations like Ca2+
, Cu2+
, or Zn2+
at various 24
concentrations were added to the reaction mixture to study their effect on the phosphorylation 25
reactions. 26
Homology structure modeling of the archaeal FHA domain protein 27
The biochemical and genetic functions of archaeal FHA domain proteins have not yet 28
been identified experimentally. The structure of the FHA domain of ST0829 was modeled 29
computationally using the automated comparative protein modeling web server 30
SWISS-MODEL (2) according to our previously published procedures (3) and the structure of 31
Rad53 (16). 32
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
7
1
RESULTS 2
S. tokodaii strain 7 contains a group of Ser/Thr protein kinases and an FHA 3
domain protein 4
Using a blast assay, a group of proteins in the archaeon S. tokodaii strain 7 was 5
discovered to contain conserved amino acid residues. As shown in Fig. 1A, the group 6
of proteins, including ST1565, contains several conserved domains of a typical 7
Ser/Thr protein kinase. For example, the proteins contained DVKPSN catalytic loop; 8
DFG motif; and conserved K166, D287, and D314 residues, indicating that these 9
proteins could be typical Ser/Thr protein kinases. On the other hand, as shown in Fig. 10
1B, an S. tokodaii protein, ST0829, contains a typical FHA domain in its C-terminus 11
and several conserved domain residues similar to those found in the proteins of the 12
pathogen Mycobacterium tuberculosis. A Zn finger-Ran BP domain is situated in the 13
N-terminus of ST0829 (Fig. 1B). 14
Archaeal Ser/Thr protein kinase physically interacts with an FHA domain 15
protein 16
To determine if the archaeal FHA domain protein, ST0829, was a substrate of its 17
protein kinase, ST1565, we examined the physical interaction between these two 18
proteins. As shown in Fig. 2A, in our bacterial two-hybrid experiment, a positive 19
co-transformant (CK+) grew on a selective screening medium, but the negative 20
co-transformant (CK-) did not grow at all. Moreover, the co-transformant of 21
ST1565/ST0829 grew well on the selective screening medium, providing that ST1565 22
interacted with ST0829. No growth was observed for the self-activation controls of 23
ST0829 (Fig. 2A). In addition, an unrelated ABC family kinase, ST1652, was unable 24
to interact with ST0829 because no growth was observed for their co-transformant 25
strain (Fig. 1A). To ascertain the interaction, a GST pull-down/Western blotting assay 26
was conducted. As shown in Fig. 2B, His-tagged ST0829 protein could be readily 27
pulled down by the GST-tagged ST1565 kinase protein. GST co-incubated with 28
his-tagged ST1565 did not produce any specific bands (Fig. 2B). 29
The physiological significance of these in vitro interactions was studied with a 30
co-immunoprecipitation (Co-IP) experiment. An in vivo physical interaction between 31
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
8
ST1565 and ST0829 was examined using Protein A beads that were first conjugated 1
with antibody raised against ST1565. In our Co-IP assay, as shown in Fig. 2C, 2
ST0829 clearly associated with ST1565 as an additional specific hybridization signal 3
was detected when compared with a negative control (no beads added). Therefore, 4
ST1565 kinase physically interacted with ST0829 FHA domain protein under 5
archaeal physiological conditions. 6
ST1565 protein kinase prefers Mn2+
as its cofactor and has conserved amino acid 7
residues 8
To establish which metal ion is essential for the optimal activity of ST1565, the 9
activating effects of several divalent metal ions on its auto-phosphorylation activity 10
were tested. As shown in Fig. 3A, among five metal ions, the protein kinase 11
demonstrated the best activity when Mn2+
was added into the reaction. In comparison, 12
very low activities were observed when several other metal ions such as Ni2+
, Zn2+
, 13
Mg2+
, or Ca2+
were added (Fig. 3A). 14
As shown in Fig. 1A, using a blast assay, several conserved residues, such as 15
K166, D287, D314, T326, and T329, associated with potential protein kinases in S. 16
tokodaii were uncovered. These residues were also situated within or close to the 17
major functional domains of the Ser/Thr protein kinase, for example, the catalytic 18
loop and DFG motif, as shown in Fig. 1A (lower panel). When these mutant proteins 19
were purified and their auto-phosphorylation activities compared with the wild-type 20
protein, several amino acid substitution mutants, including ST1565-K166A, 21
ST1565-D287A, ST1565-D314A, and ST1565-T329A, retained very weak activities, 22
as shown in Fig. 3B. One mutant, ST1565-T326A, demonstrated a higher 23
auto-phosphorylation activity than the wild-type protein (Fig. 3B). In a further 24
time-course experiment as shown in Fig. 3C, ST1565-T326A demonstrated a stepwise 25
increase in auto-phosphorylation activity as the reaction time increased, it achieving a 26
final rate of 2.0 nmol 23
p/min.mg. In contrast, the top rate for the wild-type protein 27
was at most 1.0 nmol 23
p/min.mg, although it reached this level of activity within a 28
shorter time frame (20 min). 29
Therefore, several residues of ST1565 protein kinase proved to be essential for 30
auto-phosphorylation activities, but the T326 residue of ST1565 proved otherwise. 31
Ser/Thr protein kinase ST1565 phosphorylated the FHA domain protein ST0829 32
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
9
The physical interaction of ST1565 with ST0829 suggests a functional correlation 1
between them. To detect if ST0829 could be phosphorylated by ST1565, we assayed 2
the activity under different metal ions. As shown in Fig. 4A, no obvious 3
phosphorylation activity was observed if no metal ion was added in the reaction. No 4
activity was also observed for unrelated kinase ST1652 (Supplemental Fig. 1S). Mn2+
5
clearly stimulated the phosphorylation of ST0829 by ST1565, which was consistent 6
with the auto-phosphorylation of ST1565. Additionally, Mg2+
also demonstrated a 7
stimulating activity (Fig. 4A), although a lesser content than Mn2+
. 8
To examine the optimal condition for the kinase activity of the protein from the 9
extremely thermoacidophilic archaeon, we examined the phosphorylation activities 10
under different temperature and pH conditions. As shown in Fig. 4, when ST0829 was 11
used as substrate, the relative kinase activity of ST1565 had an optimal temperature of 12
approximately 45°C (Fig. 4B), and an optimal pH range between 5.5 and 7.5 (Fig. 13
4C), which were consistent with the physiological environment of the archaeon. 14
Effects of essential residues of ST1565 and ST0829 on the kinase activity 15
To characterize the effects of the conserved residues of ST1565 on its protein 16
kinase, its several amino acid substitution mutants, including ST1565-K166A, 17
ST1565-D287A, ST1565D314A, ST1565-T326A, and ST1565-T329A, were purified 18
and their kinase activities were assayed. As shown in Fig. 5A, four amino acid 19
substitution mutant proteins, namely ST1565-K166A, ST1565-D287A, 20
ST1565-D314A, and ST1565-T329A, lost the kinase activities as no phosphorylated 21
ST0829 was observed. Unexpectedly, an approximately 5.5-fold higher activity was 22
observed for the mutant ST1565-T326A, indicating that the residue negatively 23
regulated the kinase activity of ST1565 on the substrate protein ST0829 (Fig. 5A). 24
This most likely is because the ST1565-Thr326 residue could compete with the 25
phosphate group for the active center of ST1565, and thus partially inhibiting both 26
auto-phosphorylation and transphosphorylation activities. This was consistent with the 27
earlier observation that auto-phosphorylation activity of ST1565-T326A was higher 28
than that of wild-type ST1565 protein (Fig. 3B). On the other hand, when examining 29
the effects of several conserved ST0829 residues on the kinase activity of ST1565, a 30
relatively reduced amount of the ST0829 amino acid substitution mutant proteins was 31
phosphorylated when compared with the ST0829 wild-type protein (Fig. 5B). 32
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
10
Therefore, all aforementioned residues of ST0829 negatively affected the kinase 1
activity of ST1565 protein. 2
Several ST0829 mutants lost their interactions with the ST1565 protein kinase 3
From the blast assay as shown in the Fig. 1B, the group of FHA 4
domain-containing proteins in S. tokodaii contains several conserved residues, such as 5
R164, S178, T199, and N200. These residues were also situated within the potential 6
FHA domain of ST0829 as shown in Fig. 1B (lower panel). To examine if these 7
ST0829 conserved residues play any importance in the interaction with ST1565, we 8
conducted a bacterial two-hybrid experiment. As shown in Fig. 6A, the 9
co-transformants of several ST0829 amino acid substitution mutants with ST1565 10
demonstrated only very weak growth on the selective screening medium, while the 11
wild-type ST1565/ST0829 con-transformant grew favorably. Additionally, a positive 12
co-transformant (CK+) grew on the selective screening medium, but a negative 13
co-transformant (CK-) did not grow at all. No growth was observed for the 14
self-activation controls of all ST0829 mutants (Fig. 6A). This result indicated that 15
several ST0829 mutants lost their interactions with ST1565. 16
Using the automated comparative protein modeling web server SWISS-MODEL 17
(23) and the Rad53 FHA domain (PDB ID: 2JQI) as a template, a structural modeling 18
of the FHA domain of ST0829 (Fig. 6B) was performed. As shown in Fig. 6B, several 19
mutant residues were situated at the edge of the FHA domain, indicating that these 20
residues could be involved in the interaction between ST0829 and ST1565. 21
DISCUSSION 22
Protein phosphorylation on serine, threonine, and tyrosine is one of the most 23
important post-translational modifications in eukaryotes and bacteria (30). However, 24
specific information concerning Ser/Thr protein kinase and its partner substrate in 25
Archaea, the third domain of life, is lacking. In this study, we have successfully 26
characterized an archaeal Ser/Thr protein kinase and its partner substrate. In 27
particular, the archaeal FHA domain protein was, for the first time, found to be the 28
substrate phosphorylated by a typical Ser/Thr protein kinase. Moreover, the conserved 29
sites for both the kinase and the FHA protein were identified through a series of 30
mutation assays. Several essential residues for the kinase activities were characterized 31
and a negative regulating site of Threonine-326 was found. A number of conserved 32
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
11
residues in ST0829 proved important for its interactions with ST1565 and for the 1
kinase activities. These first-hand data now offer important clues that promote our 2
understanding of not only the structural or functional characteristics of the archaeal 3
proteins, but also of a fundamental signaling mechanism in all three domains, 4
eukaryote, bacteria, and archaea. 5
The thermoacidophilic archaeon S. tokodaii str.7 grows under high temperature 6
and low pH conditions. We discovered that the archaeal Ser/Thr protein kinase 7
ST1565 had an optimal temperature of 45°C and a pH range of 5.5-7.5, which was 8
consistent with its physiological environments. ST1565 preferred divalent cations as 9
its cofactor for auto-phosphorylation and substrate phosphorylation, which was a 10
similar feature shared with some bacterial and eukaryotic Ser/Thr protein kinases 11
(11). This indicated that the third domain Archaea retained a general catalytic 12
mechanism for protein phosphorylation as in the other two domains, Eucarya and 13
Bacteria. 14
Several ORFs potentially encoding eukaryote-like protein kinases have been 15
identified in members of Archaea (17, 28) based on computer assays. However, at 16
present, only very few proteins have actually been demonstrated to possess the 17
catalytic activity implied from their sequence (18). There is also no report showing 18
that the genome of any archaeon contains a typical eukaryote-like Ser/Thr protein 19
kinase family. In the present study, we have characterized a group of this kind of 20
archaeal kinase, although the level of overall sequence identity was extremely low. As 21
shown in Fig. 1, conserved residues in the archaeon were found that corresponded to 22
those of eukaryotic Ser/Thr kinase (11), that are responsible for ATP binding, 23
phospho-transfer, metal ion-binding and auto-phosphorylation. The importance of 24
these residues in the kinase function was clear, since mutations of these sites resulted 25
in the loss of kinase activity. 26
Little is known regarding the structural or functional characteristics of archaeal 27
eukaryote-like Ser/Thr protein kinases. Our results demonstrated that the archaeal 28
kinase contains a general and fundamental conservation with corresponding 29
eukaryotic proteins. However, an unexpected finding was the totally different effect of 30
two mutations situated in the activation loop of the enzyme on the protein kinase 31
function (Fig. S1). In contrast to the loss of the activity by the mutation at Thr329, the 32
mutation of Thr326 obviously stimulated the auto-phosphorylation activity (Fig. 3), 33
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
12
and tremendously improved the phosphorylation activity (about 5.5-fold) of the FHA 1
domain substrate (Fig. 5). Thus, these two Thr residues contribute in totally different 2
ways to the activity of the ST1565 protein kinase. In contrast to the negative 3
regulation of Thr326, Thr329 was shown to be essential for both auto-phosphorylation 4
and transphosphorylation activities of ST1565 (Fig. 3 and Fig. 5). This implies that 5
Thr329 is an important activation site for the kinase function. This finding offers 6
important clues, not only to the structural characteristics of archaeal protein kinases, 7
but also to the origins and evolution of a fundamentally important regulatory 8
mechanism in eukaryote. 9
Recently, FHA domain-containing protein has been proposed to interact with a 10
protein partner in a process regulated by reversible protein phosphorylation in both 11
eukaryote and bacteria (4). However, the existence of FHA domain proteins was 12
unknown in the members of archaea and there have been no reports of experimental 13
identification of any binding partner of any archaeal FHA domain (21). In this study, 14
we found several conserved FHA-like genes in the extreme acidothermophilic 15
archaeon Sulfolobus species (Fig. 1B). Based on the structure of Rad53 (16), using 16
homology structure modeling, we obtained a structure of archaeal FHA domain (Fig. 17
6B). The conserved sites with FHA domain protein were also confirmed as 18
essential for interaction and phosphorylation with the ST1565 kinase. All of the FHA 19
mutant proteins in our study partially lost phosphorylation activities by protein kinase 20
(Fig. 5). Interestingly, in contrast with the wild-type protein, these mutants also lost 21
their capacity to interact with protein kinase, according to our bacterial two-hybrid 22
experiment (Fig. 6A). This demonstrated that these extensively conserved FHA 23
domain sites might be important for the recognition and phosphorylation of FHA 24
protein by its corresponding Ser/Thr protein kinase in all three domains of Eukaryota, 25
Bacteria, and Archaea. 26
Numerous phosphorylated archaeal proteins have already been reported. However, 27
the cellular impacts of these phosphorylations are largely unknown. The FHA domain 28
protein ST0829, which we have characterized as a partner substrate of protein kinase 29
ST1565, is a potential transcriptional regulator (Fig. 1B). It contains an N-terminal 30
Zn-finger RanBP domain, which is usually responsible for DNA-binding protein. Our 31
result suggests that the phosphorylation signal might participate in the transcriptional 32
regulation in Archaea. This may be vital for the extreme acidothermophilic archaeon 33
for appropriate adaptive responses to their environmental cues. These are also the first 34
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
13
data to show the possibility of the Ser/Thr protein kinase signaling in coupling with 1
transcriptional regulation in an archaeon. However, further detailed study remains to 2
be performed. 3
In conclusion, we have presented primary data showing that a protein kinase 4
interacts with and phosphorylates its FHA domain protein in the third domain, 5
Archaea. The information gathered on the structure, function, and protein-protein 6
interaction of archaeal proteins offers important clues for understanding the 7
mechanisms by which these unique organisms adapt to their extreme environments, 8
and also provides a way to trace the origins and evolution of a fundamental biological 9
signaling transduction mechanism. 10
ACKNOWLEDGEMENTS 11
We thank Prof. Yulong Shen (Shandong University, China) for offering the 12
archaeal strain. This work was supported by the National Natural Science Foundation 13
of China, the 973 Program (2006CB504402), New Century Excellent Talents Fund of 14
the Ministry of Education of China (NECT-06-0664), Doctoral Fund of Ministry of 15
Education of China (200805040004), and the China National Fundamental Fund of 16
Personnel Training (J0730649). 17
REFERENCES 18
1. Aivaliotis, M., B. Macek, F. Gnad, P. Reichelt, M. Mann, and D. Oesterhelt. 2009. 19
Ser/Thr/Tyr protein phosphorylation in the archaeon Halobacterium salinarum—A 20
representative of the third domain of life. PLoS ONE 4(3):e4777. 21
2. Arnold, K., L. Bordoli, J. Kopp, and T. Schwede. 2006. The SWISS-MODEL 22
workspace: a web-based environment for protein structure homology modeling. 23
Bioinformatics 22:195-201. 24
3. Cui, T., L. Zhang, X. Wang, and Z. G. He. 2009. Uncovering new signaling proteins 25
and potential drug targets through the interactome analysis of Mycobacterium 26
tuberculosis. BMC Genomics 10:118. 27
4. Durocher, D., and S. P. Jackson. 2002. The FHA domain. FEBS Lett 513:58–66. 28
5. Durocher, D., J. Henckel, A. R. Fersht, and S. P. Jackson. 1999. The FHA domain is 29
a modular phosphopeptide recognition motif. Mol Cell 4:387–394. 30
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
14
6. Falke, J. J., R. B. Bass, S. L. Butler, S. A. Chervitz, and M. A. Danielson. 1997. The 1
two-component signaling pathway of bacterial chemotaxis: a molecular view of signal 2
transduction by receptors, kinases, and adaptation enzymes. Annu Rev Cell Dev Biol 3
13:457–512.; 423. 4
7. Gill, S. C., and P. H. Hippel. 1989. Calculation of protein extinction coefficients from 5
amino acid sequence data. Anal Biochem 182:319-326. 6
8. Hofmann, K., and P. Bucher. 1995. The FHA domain: a putative nuclear signalling 7
domain found in protein kinases and transcription factors. Trends Biochem Sci 8
20:347–349. 9
9. Hunter, T. 1995. Protein kinases and phosphatases: the yin and yang of protein 10
phosphorylation and signalling. Cell 80:225–236. 11
10. Kennelly, P. J. 2002. Protein kinases and protein phosphatases in prokaryotes: a genomic 12
perspective. FEMS Microbiol Lett 206:1–8. 13
11. Kornev, A. P., N. M. Haste, S. S. Taylor, and L. F. Ten Eyck. 2006. Surface 14
comparison of active and inactive protein kinases identifies a conserved activation 15
mechanism. Proc Natl Acad Sci U S A 103(47):17783–17788. 16
12. LaRonde-LeBlanc, N., and A. Wlodawer. 2004. Crystal structure of A. fulgidus Rio2 17
defines a new family of serine protein kinases. Structure (Cambridge) 12:1585–1594. 18
13. LaRonde-LeBlanc, N., T. Guszczynski, T. Copeland, and A. Wlodawer. 2005. 19
Structure and activity of the atypical serine kinase Rio1. FEBS J 272:3698–3713. 20
14. LaRonde-LeBlanc, N., T. Guszczynski, T. Copeland, and A. Wlodawer. 2005. 21
Autophosphorylation of Archaeoglobus fulgidus Rio2 and crystal structures of its 22
nucleotide–metal ion complexes. FEBS J 272:2800–2810. 23
15. LaRonde-LeBlanc, N., and A. Wlodawer. 2005. The RIO kinases: An atypical protein 24
kinase family required for ribosome biogenesis and cell cycle progression. Biochimica 25
et Biophysica Acta 1754:14–24. 26
16. Lee, H., C. Yuan, A. Hammet, A. Mahajan, E. S. Chen, M. R. Wu, M. I. Su, J. 27
Heierhorst, and M. D. Tsai. 2008. Diphosphothreonine-specific interaction between an 28
SQ/TQ cluster and an FHA domain in the Rad53-Dun1 kinase cascade. Mol Cell 29
30:767–778. 30
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
15
17. Leonard, C. J., L. Aravind, and E. V. Koonin. 1998. Novel families of putative protein 1
kinases in bacteria and archaea: evolution of the “eukaryotic” protein kinase superfamily. 2
Genome Res 8:1038–1047. 3
18. Lower, B. H., and P. J. Kennelly. 2003. Open Reading Frame sso2387 from the 4
archaeon Sulfolobus solfataricus encodes a polypeptide with protein-serine kinase 5
activity. J Bacteriol 185:3436–3445. 6
19. Lower, B. H., M. B. Potters, and P. J. Kennelly. 2004. A Phosphoprotein from the 7
archaeon Sulfolobus solfataricus with protein-serine/Threonine kinase activity. J 8
Bacteriol 186:463–472. 9
20. Manning, G., D. B. Whyte, R. Martinez, T. Hunter, and S. Sudarsanam. 2002. The 10
protein kinase complement of the human genome. Science 298:1912–1934. 11
21. Pallen, M., R. Chaudhuri, and A. Khan. 2002. Bacterial FHA domains：neglected 12
players in the phospho-threonine signalling game? Trends Microbiol 10(12):556–563. 13
22. Ptacek, J., G. Devgan, G. Michaud, H. Zhu, X. Zhu, J. Fasolo, H. Guo, G. Jona, A. 14
Breitkreutz, R. Sopko, R. R. McCartney, M. C. Schmidt, N. Rachidi, S. J. Lee, A. S. 15
Mah, L. Meng, M. J. Stark, D. F. Stern, C. D. Virgilio, M. Tyers, B. Andrews, M. 16
Gerstein, B. Schweitzer, P. F. Predki, and M. Snyder. 2005. Global analysis of protein 17
phosphorylation in yeast. Nature 438:679–684. 18
23. Rudolph, J., and D. Oesterhelt. 1995. Chemotaxis and phototaxis require a CheA 19
histidine kinase in the archaeon Halobacterium salinarum. EMBO J 14:667–673. 20
24. Rudolph, J., N. Tolliday, C. Schmitt, S. C. Schuster, and D. Oesterhelt. 1995. 21
Phosphorylation in halobacterial signal transduction. EMBO J 14:4249–4257. 22
25. Shi, L., M. Potts, and P. J. Kennelly. 1998. The serine, threonine, and/or 23
tyrosine-specific protein kinases and protein phosphatases of prokaryotic organisms: A 24
family portrait. FEMS Microbiol Rev 22:229–253. 25
26. Skorko, R. 1984. Protein phosphorylation in the archaebacterium Sulfolobus 26
acidocaldarius. Eur J Biochem 145:617–622. 27
27. Skorko, R., J. Osipiuk, and K. O. Stetter. 1989. Glycogen-bound polyphosphate kinase 28
from the archaebacterium Sulfolobus acidocaldarius. J Bacteriol 171:5162–5164. 29
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
16
28. Smith, S. C., B. McCartney, P. J. Kennelly, and M. Potts. 1997. Proteintyrosine 1
phosphorylation in the Archaea. J Bacteriol 179:2418–2420. 2
29. Spudich, J. L., and W. Stoeckenius. 1980. Light-regulated retinal-dependent reversible 3
phosphorylation of Halobacterium proteins. J Biol Chem 255:5501–5503. 4
30. Stock, J. B., A. J. Ninfa, and A. M. Stock. 1989. Protein phosphorylation and regulation 5
of adaptive responses in bacteria. Microbiol Rev 53:450–490. 6
31. Szurmant, H., and G. W. Ordal. 2004. Diversity in chemotaxis mechanisms among the 7
bacteria and archaea. Microbiol Mol Biol Rev 68:301–319. 8
32. Tahara, M., A. Ohsawa, S. Saito, and M. Kimura. 2004. In vitro phosphorylation of 9
initiation factor 2 alpha (aIF2 alpha) from hyperthermophilic archaeon Pyrococcus 10
horikoshii OT3. J Biochem. 135: 479-485. 11
33. Yaffe, M. B., and A. E. Elia. 2001. Phosphoserine/threonine-binding domains. Curr Opin 12
Cell Biol 13:131–138. 13
34. Zhang, L., L. Zhang, Y. Liu, S. Yang, C. Gao, H. Gong, Y. Feng, and Z. G. He. 2009. 14
Archaeal eukaryote-like Orc1/Cdc6 initiators physically interact with DNA polymerase 15
B1 and regulate its functions. Proc Natl Acad Sci U S A 106:7792-7797. 16
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
17
FIGURE LEGENDS 1
Fig. 1 Blast assay for a group of archaeal Ser/Thr protein kinases and an FHA 2
domain protein in S. tokodaii strain 7. (A) The predicted protein product of ORF 3
ST1565 from the genome of S. tokodaii contains conserved sequence motifs of typical 4
eukaryote-like Ser/Thr protein kinases. The positions of plausible candidates for the 5
conserved sequence motifs or residues, characteristic of members of the eukaryotic 6
superfamily of protein kinases are indicated at the residue sites. (B) The predicted 7
protein product of ORF ST0829 contains conserved sequence motifs of FHA domain 8
(EmbR of Mycobacterium tuberculosis) and Zn finger RanBP domain. The positions 9
of the conserved sequence motifs are indicated with the residue sites. 10
Fig. 2 Archaeal Ser/Thr protein kinase physically interacted with an FHA 11
domain protein in S. tokodaii strain 7. (A) Bacterial two-hybrid assay (Stratagene) 12
for the interaction between ST1565 and ST0829, which was performed as described in 13
the “Materials and Methods”. Left panel, plate minus streptomycin (str) and 5 mM 14
3-amino-1,2,4-triazole (3-AT); middle panel, plate plus str and 5 mM 3-AT; right 15
panel, an outline of the plates. CK+, co-transformant containing pBT-LGF2 and 16
pTRG-Gal11P as a positive control; CK-, co-transformant containing pBT and pTRG 17
as a negative control. (B) Pull-down assays. Normalized GST or GST-ST0829 18
proteins were combined with his-tagged-ST1565 proteins. The mixtures were 19
subsequently purified using the GST-affinity assay as described in the 20
“Materials and Methods”. All samples were subjected to SDS-PAGE and the protein 21
bands were transferred to a nitrocellulose membrane for Western blot analysis. The 22
hybridization signal was recorded by photography. (C) Co-IP assays. Exponentially 23
growing cells of S. tokodaii were harvested, resuspended, and lysed. Co-IPs were 24
performed by incubating 10 µL of archaeal cell extract with 3 µL of ST0829 antiserum 25
for 3 h at 4 °C. A 20-µL slurry of protein A Sepharose was added, and incubation was 26
continued for another hour. Immune complexes were collected, and the beads were 27
washed with buffer. Finally, the beads were resuspended in SDS/PAGE sample 28
buffer. After boiling, the samples were analyzed by Western blotting using 29
anti-ST1565 antibody. 30
Fig. 3 Assays for ion-dependent auto-phosphorylation activity of archaeal 31
Ser/Thr protein kinase and its conserved activity sites. Analysis of the protein 32
kinase activities was performed as described under “Materials and Methods”. 33
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
18
Phosphorylation was carried out in the buffer (20 mM Hepes [pH 7.4], 10 mM MgCl2, 1
and 10 mM MnCl2) containing 300 µCi [γ-32
P]ATP for 30 min at 55 °C. The reaction 2
was stopped with sample buffer and proteins were separated on 10% SDS-PAGE and 3
analyzed by autoradiography. (A) Effect of different ions on the activities of protein 4
kinase. Mg2+
, Mn2+
, and divalent cations like Ca2+
, Cu2+
, or Zn2+
of various 5
concentrations were added in the reaction mixture to study their effect on the 6
phosphorylation reaction. (B) Protein kinase activities of various ST1565 mutant 7
proteins. (C) Time course assays for the phosphorylation of ST1565 and 8
ST1565-T326A. 9
10
Fig. 4 Effect of ions, temperature, and pH on the kinase activities of archaeal 11
Ser/Thr protein kinase. Analysis of the protein kinase activities of ST1565 on the 12
phosphorylation of ST0829 was performed as described in the 13
“Materials and Methods”. Phosphorylation was carried out in the buffer (20 mM Hepes 14
[pH 7.4], 10 mM MgCl2, and 10 mM MnCl2) containing 300 µCi [γ-32
P]ATP for 30 15
min. The proteins were separated on 10% SDS-PAGE and analyzed by 16
autoradiography. (A) Effect of different ions on the activities of protein kinase. Mg2+
, 17
Mn2+
, and divalent cations, like Ca2+
, Cu2+
, or Zn2+
of various concentrations were 18
added in the reaction mixture to study their effect on the phosphorylation reaction. (B) 19
Effect of different temperatures on the activities of protein kinase. (C) Effect of pH on 20
the activities of protein kinase. 21
Fig. 5 Effect of mutations in conserved amino acid residues of the archaeal 22
Ser/Thr protein kinase and FHA protein on the phosphorylation activities. 23
Various archaeal Ser/Thr protein kinase and FHA mutants were prepared as described 24
under “Materials and Methods”. Analysis of the kinase activities of ST1565 on the 25
phosphorylation of ST0829 was carried out in the buffer (20 mM Hepes [pH 7.4], 10 26
mM MgCl2, and 10 mM MnCl2) containing 300 µCi [γ-32
P]ATP for 30 min at 55 °C. 27
The proteins were separated on 10% SDS-PAGE and analyzed by autoradiography. 28
(A) Effects of conserved sites of the archaeal Ser/Thr protein kinase on the 29
phosphorylation activities of the FHA protein. (B) Effects of conserved sites of the 30
FHA protein on its phosphorylation activities by the archaeal Ser/Thr protein kinase. 31
Fig. 6 Assays for the interaction between the archaeal Ser/Thr protein kinase 32
and FHA protein mutants. (A) Bacterial two-hybrid assay (Stratagene) for the 33
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
19
interactions between ST0829 mutants and ST1565, which was performed as described 1
under “Materials and Methods”. CK+, co-transformant containing pBT-LGF2 and 2
pTRG-Gal11P as a positive control; CK-, co-transformant containing pBT and pTRG 3
as a negative control. (B) The position and presumptive function of conserved 4
residues of ST0829 FHA domain. The structure of the FHA domain was obtained 5
using the homology modeling method as described under “Experimental procedures”. 6
on April 24, 2020 by guest
http://jb.asm.org/
Dow
nloaded from
