Volume 270,
Number 4,
Issue of January 27, 1995 pp. 1833-1842
©1995 by The American Society for Biochemistry and Molecular Biology, Inc.
Structural
and Functional Studies of the Intracellular Tyrosine Kinase MATK Gene
and Its Translated Product (*)
(Received for publication, June 21, 1994; and in revised form, October 14, 1994)
Shalom
Avraham ,
Shuxian
Jiang,
Setsuo
Ota ,
Yigong
Fu,
Bijia
Deng,
Lisa
L.
Dowler
(1),
Robert A.
White
(1),
Hava
Avraham (§)
From the Division of Hematology/Oncology, New England
Deaconess Hospital, Harvard Medical School, Boston, Massachusetts 02215
and the Section of Genetics, Children's Mercy
Hospital, UMKC School of Medicine, Kansas City, Missouri 64108
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
FOOTNOTES
ACKNOWLEDGEMENTS
REFERENCES
ABSTRACT
We recently cloned the cDNA which encodes a novel
megakaryocyte-associated tyrosine kinase termed MATK. In this study, we
have cloned and characterized the human MATK gene as well as the murine
homolog of human MATK cDNA and performed functional studies of its
translated product. Comparison of the deduced amino acid sequences of
human and murine MATK cDNAs revealed 85% homology, indicating that MATK
is highly conserved in mouse and human. The human gene consists of 13
exons interrupted by 12 introns. The genetic units which encode the SH3
and SH2 domains are located on separate exons. The putative ATP binding
site (GXGXXG) is localized on exon 7, and the entire
catalytic domain is subdivided into seven
exons(7, 8, 9, 10, 11, 12, 13) .
Somatic cell hybrid analysis indicated that human MATK gene is located
on chromosome 19 while the murine Matk gene is located on
chromosome 10. The immediate 5`-flanking region was highly rich in GC
sequences, and potential cis-acting elements were identified including
several SP1, GATA-1, APRE, and APRE1. Antisense oligonucleotides
directed against MATK mRNA sequences significantly inhibited
megakaryocyte progenitor proliferation. Functional studies indicated
that MATK can phosphorylate the carboxyl-terminal conserved tyrosine of
the Src protein. These results support the notion that MATK acts as a
regulator of p60
in megakaryocytic
cells and participates in the pathways regulating growth of cells of
this lineage.
INTRODUCTION
Several Src-related protein tyrosine kinases are known to
function in the regulation of proliferation and maturation of
hematopoietic cells(1, 2, 3, 4) . Fyn(5) , Lck(6) , and Zap-70 (7) play important roles in T-cell receptor signaling. A
similar signaling mechanism exists in B-cells and involves
Lyn(8) . Deficient expression of the tyrosine kinase ATK/MPK
results in the syndrome of human x-linked
agamma-globulinemia(9, 10) . Furthermore, the
oncogenic potential of the Src family protein tyrosine kinases was
found to be associated with their enzymatic
activation(4, 5, 6, 11, 12) .
This enzymatic activity is primarily regulated through the
phosphorylation of a conserved carboxyl-terminal tyrosine residue (3, 4, 11, 12) . Phosphorylation of
this residue reduces kinase activity, while dephosphorylation by
protein tyrosine phosphatases increases kinase activity.
Phosphorylation of the regulatory tyrosine residue appears to involve
Csk, a recently identified intracellular protein tyrosine kinase
distinct from the known members of the Src family. Csk was initially
purified from rat brain (13) and later cloned from human and
chicken tissues(14, 15, 16) . The protein
lacks an autophosphorylation site within its kinase domain and a
carboxyl-terminal equivalent of Tyr-527. Csk phosphorylates several Src
family protein tyrosine kinases at their carboxyl-terminal tyrosines
thereby altering their enzymatic
function(17, 18, 19, 20) .
Csk-deficient mouse embryos yields a lethal
phenotype(21, 22) .
We have recently identified and
characterized a novel intracellular tyrosine kinase, termed MATK, (
)which shares
50% homology to Csk and is predominantly
expressed in cells of megakaryocytic lineage and brain(23) .
The MATK cDNA clone encodes a polypeptide of 507 amino acids. Sequence
comparisons also indicate that MATK contains Src homology (SH) region 2
and region 3 domains but lacks the NH
-terminal
myristylation signal, the negative regulatory tyrosine (Tyr-527), and
the autophosphorylation site (Tyr-416) corresponding to those found in
Src. Expression of MATK mRNA was up-regulated in megakaryocytic cells
induced to differentiate by the phorbol ester PMA(23) .
In
the present report, we have cloned and characterized the human MATK
gene and the mouse homolog of the human MATK cDNA. We have determined
the exon-intron organization of the human MATK gene and have mapped its
putative transcription initiation site. The putative promoter region
was sequenced, and potential cis-acting elements were identified. The
chromosomal location of human MATK and murine Matk was
determined. In addition, functional studies of the MATK protein were
performed. We observed that MATK can phosphorylate the
carboxyl-terminal tyrosine of Src. Furthermore, the generation of
megakaryocyte colonies (CFU-MK) from marrow CD34
progenitor cells treated with MATK antisense oligonucleotides was
significantly reduced compared to the sense-treated CD34
cells or untreated control cells. These studies suggest that MATK
may play an important role in signal transduction pathways of
megakaryocytic cells, particularly those involved in their growth and
maturation.
EXPERIMENTAL PROCEDURES
Materials
Chemical reagents were purchased from
Sigma. The
-EMBL-3 human genomic library was kindly obtained from
Dr. Stuart Orkin (Children's Hospital, Harvard Medical School,
Boston). The
gtll mouse brain cDNA library was obtained from
Clontech (Palo Alto, CA). Restriction endonucleases, modifying enzymes,
terminal deoxynucleotidyl transferase, random priming kits, and
Sephadex G-25 quickspin columns were purchased from Pharmacia Biotech
Inc. and New England Biolabs (Beverly, MA). The primers for polymerase
chain reaction (PCR), RNA-PCR, and for sequencing, were synthesized by
an automated DNA synthesizer (Applied Biosystems, model 394). The PCR
and RNA-PCR kits were obtained from Perkin-Elmer Cetus. Sequenase and
random primer kits were obtained from U. S. Biochemical Corp.
(Cleveland, OH) and RNA isolation kits from Stratagene (La Jolla, CA).
The antibodies for Csk were kindly obtained from Dr. Andre Veillette
(McGill University, Montreal, Canada).
Cells
Human bone marrow was obtained by aspiration
from the iliac crest of normal donors following informed consent as
described previously(24) . After two washes with sterile 1
phosphate-buffered saline, the cells were resuspended in RPMI
1640 medium with 7.5% platelet poor plasma (PPP),
penicillin/streptomycin (P/S), and L-glutamine, seeded onto
T-75 tissue culture flasks (Corning, Corning, NY), and incubated at 37
°C in 5% CO
. CD34
bearing marrow
progenitor cells were purified from heparinized bone marrow aspirates
using immunomagnetic beads coated with anti-CD34 monoclonal antibody as
described(24) . The CD34
cell population was
95-98% pure as judged by labeling with fluorescein-conjugated
CD34 antibodies after an overnight recovery in RPMI plus 7.5% PPP. The CMK cell line (provided by Dr. T. Sato) (25) and the
Dami cell line (provided by Dr. S. Greenberg) (26) have
authentic properties of cells of megakaryocytic lineage. The CMK and
Dami cell lines were cultured in RPMI 1640 medium with 10% fetal calf
serum. The TPA301 cell lines were cultured in Dulbecco's modified
Eagle's medium with 10% fetal calf serum. HeLa cells were
obtained from the ATCC and cultured in RPMI 1640 medium with 10% fetal
calf serum. Megakaryocytic cells were induced to differentiate by
treatment with PMA. PMA was dissolved in dimethyl sulfoxide and stored
at -20 °C until use, when it was diluted in RPMI 1640 medium
and used at 10 ng/ml.
Antisense Oligonucleotide Synthesis and Cell
Treatment
Modified 18-mer oligonucleotides were synthesized by
Genosys Biotechnologies, Inc. (The Woodlands, Texas), precipitated, and
resuspended in RPMI 1640 as described
previously(24, 27) . MATK antisense AS1 5`-AAC CAG AGA
GCC TCG CCC CGC-3` corresponded to nucleotides +4 to +24. All
experiments were carried out with the corresponding sense 5`-GCG GGG
CGA GGC TCT CTG GTT-3` and scrambled sequence controls. CD34
cells were incubated at a concentration of 1
10
cells/ml in serum-deprived medium. Medium
contained iron-saturated human transferrin (300 µg/ml), insulin
(100 ng/ml), calcium chloride (28 µg/ml), deionized bovine serum
albumin (2%), 6.14 mg of oleic acid, and 7.4 mg of dipalmitoyl lecithin
in 10 ml of RPMI. Incubation medium was supplemented with recombinant
human interleukin-3 (100 units/ml) (R& Systems, Minneapolis, MN).
Oligonucleotides were used at a concentration of 10 mmol/liter (70
µg/ml). After 16 h of incubation at 37 °C, 5 mmol/liter
oligonucleotides were added. Cells were further incubated for an
additional 6 h and then washed in RPMI 1640 before plating or RNA
extraction, or preparation of total lysates for Western blot analysis
as described(23) .
Colony Assays
Cells were placed in the fibrin clot
culture system as described(28, 29) . Cells were
seeded at a concentration of 500 cells/0.5 ml in culture containing 10%
PPP and interleukin-3 (100 units/ml). Cultures were incubated for 12
days. Fibrin clots were fixed for 5 min with 10% neutral formalin and
reacted with platelet glycoprotein IIIa (GpIIIa) fluorescein-conjugated
monoclonal mouse antibodies to human GpIIIa (1:1000 dilution) (Dako,
Carpinteria, CA) for 30 min. The numbers of positive CFU-MK were
counted.
Reverse Transcription-Polymerase Chain
Reaction
RNA extracted from a pellet containing 1
10
CD34
cells was reverse transcribed at
42 °C for 40 min in a final volume of 50 µl as
described(23) . The 5`- and 3`-specific primers were added in
final concentrations each of 5 ng/50 µl. The mixture was subjected
to 30 amplification cycles using the Perkin-Elmer thermal cycler set as
follows: denaturation at 94 °C for 1 min, primer annealing at 55
°C for 1 min, and extension at 72 °C for 2 min.The sequence
of the MATK upstream primer was 5`-GCG GGG CGA GGC TCT CTG GTT-3`
(corresponding to position +265 to +285 bp). The nucleotide
sequence of the downstream primer was 5`-TGC GAG CAC ACC CGC CCC AAG-3`
(corresponding to position +430 to +450 bp). Primers for the
-actin message were: upstream primer 5`-ATG GAT GAT GAT ATC GCC
GCG-3` and downstream primer was 5`-CTA GAA GCA TTT GCG GTG GAC GAT GGA
GGG GCC-3` (30) . Primers specific for the c-kit message as
well as the probe for c-kit were used as described
previously(31) . The amplification products were detected by an
overnight hybridization to synthetic
P-
ATP-labeled
oligomer probes for: MATK probe 5`-GCC GTC ATG ACG AAG ATG CAA-3` and
-actin probe 5`-GAG GAG CAC CCC GTG CTG CTG A-3`. The PCR products
were analyzed as described previously (23) .
Screening of Human Liver Genomic Library
A genomic
library derived from a Sau3A1 digest of human liver DNA (32) was used to isolate 15-18 kilobase (kb) genomic DNA
clones containing the gene that encodes MATK. The human genomic library
(6
10
recombinants/screening) containing inserts
ligated into the BamHI site of the bacteriophage EMBL3 was
probed at 42 °C with an [
-
P]dCTP
(
3,000 Ci/mmol; DuPont NEN)-labeled 2.0-kb MATK cDNA probe in
hybridization buffer (50% (v/v) formamide, 0.75 M NaCl, 75
mM sodium citrate, 5
Denhardt's buffer, 0.1%
(w/v) sodium dodecyl sulfate, 1 mM EDTA, 10 mM sodium
phosphate, and 100 µg/ml salmon sperm DNA carrier). The
nitrocellulose filters were washed under conditions of high stringency
(63 °C; 30 mM NaCl, 3 mM sodium citrate, 0.1%
sodium deodecyl sulfate, 1 mM EDTA, and 10 mM sodium
phosphate, pH 7.0). Three distinct human genomic DNA clones (designated
HG-matk-1,
HG-matk-2, and
HG-matk-3) were isolated, and
DNA was prepared (33, 34) from each. These human
genomic clones were digested singularly or with various combinations of
restriction endonucleases. The DNA fragments were fractionated by
electrophoresis in 1% agarose gels and were transferred to nylon
filters (Nytran Plus, Schleicher & Schuell) (35) . The
resulting DNA blots were probed under the above conditions of high
stringency with the
P-labeled
686-bp HindIII
3`-probe, the
639-bp 5`
BglII probe, and
whole MATK cDNA. Human genomic DNA and mouse genomic DNA were isolated (36) from the human CMK cell line and mouse liver,
respectively. Samples were digested (10 µg/sample) separately with EcoRI, BamHI, HindIII, and XbaI for
4 h at 37 °C. The fragments were resolved by agarose gel
electrophoresis and were transferred to Nytran Plus membranes. The
resulting DNA blots were analyzed for hybridization under conditions of
high stringency, with 5`
BglII fragment or HindIII
3`-fragment of human MATK cDNA as probes. A
randomized and oligo(dT)-primed mouse brain cDNA library (Clontech) (6
10
recombinants/screening) was screened using the
same procedure and conditions as described above for human genomic
library.
Nucleotide Sequencing of a Human Genomic Clone That
Encodes MATK
HG-matk-1,
HG-matk-2, and
GH-matk-3
were digested with SalI, BglII, HindIII, XbaI, and EcoRI, or with a combination of these
restriction enzymes, to generate distinct DNA fragments of the clone
which were approximately 8.0 and 4.0 kb in size, respectively. These
DNA fragments were subcloned into Bluescript plasmid and sequenced in
both orientations by the chain termination method (37, 38) and by automatic sequencing using the
Pharmacia ALF sequencer. The nucleotide sequence of the first and last
250 nucleotides of each genomic fragment was determined using T7 and T3
primers (Stratagene). Based on the nucleotide sequences of the genomic
fragment being analyzed, two oligonucleotides of 21 nucleotides in
length were synthesized and used as primers to determine the contiguous
nucleotide sequence of the next 200-250 nucleotides in each
direction of the double-stranded DNA. The exon-intron organization and
the putative promoter region of the human MATK gene were determined by
this approach. The sizes of the introns were determined by two methods,
either by restriction digest mapping of DNA from the
HG-matk
clones and hybridization with specific oligonucleotide of 21
nucleotides, or by PCR using sense and antisense specific primers that
are localized between each set of two exons. The resulting DNA
sequences were analyzed at the Molecular Biology Computer Research
Resource facilities at the Dana Farber Cancer Institute (Boston, MA)
for the extent of their homology to other reported DNA sequences in the
GenBank data base. Data base searches were run against deposited
sequences in GenBank and EMBL.To determine the transcription
initiation site within the human MATK gene, primer extension analyses
were performed as described by Lee and co-workers (39) with few
modifications. CMK cells were lysed in the presence of guanidinium
isothiocyanate, and total RNA and poly(A)
RNA were
obtained by CsCl density gradient centrifugation (40) and
oligo(dT)-cellulose(41) , respectively. A sample of 36
oligonucleotides (
5 pmol) (5`-GCG GTC CCG GCT GCA CAA CTT GGA GCG
AGT TGC TCC-3`), which corresponded to residues +1 to +36 and
a sample of a second primer of 24 oligonucleotides (5`-GCT CAG GGG GCG
CCC CCG AGC CGC-3`), which corresponded to residues +87 to
+110 of the antisense strand of MATK cDNA, were separately end
labeled with [
-
P]ATP using T4
polynucleotide kinase to a specific activity of >3
10
counts/min/µg(42) . The samples were suspended in 50
mM Tris-HCl (pH 8.0) containing 3.5 mM MgCl
, 10 mM dithiothreitol, 50 mM KCl, 100 µg/ml bovine serum albumin, and 0.5 mM samples of each dNTP. CMK-derived poly(A)
mRNA
(
3 µg) and 400 units of avian myeloblastosis virus reverse
transcriptase (Life Technologies, Inc.) were added, and the samples
were incubated at 45 or 65 °C for 1 h. At the end of the incubation
period, the samples were extracted with phenol and precipitated with
ethanol, and the size of prominent radiolabeled DNA fragments extended
onto the primers were determined. For a negative control, primer
extension analyses were performed with RNA from TPA301 cells as a
template.
Chromosomal Localization of the Mouse Matk
Gene
Genomic DNAs for C57BL/6J, Mus spretus, and the
(C57BL/6J X M. spretus) F
X M. spretus backcross DNA panel were obtained from the Jackson
Laboratory, Bar Harbor, ME(43) . Southern blots and
hybridizations were performed as described previously(44) .
Genomic DNAs of C57BL/6J and M. spretus were digested
with 29 different restriction enzymes. The Southern blots were probed
with a mouse 1.8-kb Matk cDNA fragment labeled with
P using a Decaprime II Kit (Ambion). Digestion of the
backcross DNA panel with HincII, Southern blotting, and
hybridizations were carried out as described(44) .
Chromosomal Localization of the Human MATK
Gene
Genomic DNAs from the NIGMS Hybrid Mapping Panel 2 were
obtained from the NIGMS Genetic Mutant Cell Repository (Corriel Cell
Institute for Medical Research, Camden, NJ). Mapping Panel 2 consists
of DNA isolated from 24 human/rodent cell hybrids retaining one or two
human chromosomes. All but two of the hybrids retain a single intact
human chromosome. In addition, Mapping Panel 2 includes DNA samples
isolated from human, mouse, and chinese hamster cell lines (rodent
parental cell lines). Approximately 5 µg of DNA was digested for
each sample with restriction enzymes overnight. Southern blots and
hybridizations were carried out as described previously(44) .
Biochemical Analyses
For preparation of proteins
for immunoprecipitation, proteins from CMK and Dami cells were lysed in
modified RIPA buffer(20, 23) . One µg of
appropriate antibody was added to each protein sample (10 µg).
Antibodies used were rabbit anti-p60
(Upstate Biotechnology, NY), rabbit anti-MATK antibodies (23) which recognize the NH
-terminal region of the
human MATK gene product, and rabbit anti-Csk serum generated against a
TrpE fusion protein containing residues 182-450 of rat p50 Csk (a
generous gift from Dr. Andre Veillette, McGill University, Montreal,
Canada)(19) . In some experiments, we used
p60
partially purified enzyme (Upstate
Biotechnology, NY). After absorbing to protein G-Sepharose (Pharmacia),
immunoprecipitates were processed as described
previously(23, 45) . In a kinase assay,
immunoprecipitate obtained from 10 µg of total proteins, 4.5 µg
of acid-treated enolase(45) , and 4 mmol/0.74 MBq of
[
-
P]ATP were included in 25 µl of
kinase assay buffer. 5-(p-Fluorosulfonylbenzoyl) adenosine
(FSBA) was added in a final concentration of 1.0 mM as
indicated. Phosphorylation was allowed to proceed at 25 °C for 20
min, and phosphoproteins were resolved by SDS-polyacrylamide (10%) gel
electrophoresis as described(45) . Metabolic labeling,
immunoprecipitation, and immunoblots were carried out as described (23) .
RESULTS
Molecular Cloning of the Full-length Murine Matk
cDNA
Southern blot analysis of human (Fig. 1) and mouse
(data not shown) genomic DNA digested with EcoRI, HindIII, BamHI, or XabI and probed under conditions
of high stringency with either 5`
BglII fragment (639
bp in size) or HindIII
3`-fragment (689 bp in size) of
human MATK cDNA as probes, revealed a single band in each lane,
indicating that the human MATK gene and the mouse Matk gene
are highly homologous and are single genes. Therefore, a randomized and
oligo(dT)-primed mouse adult brain cDNA library was screened under
conditions of high stringency for the full-length mouse cDNA of Matk using the human MATK cDNA as a probe. Thirty clones were
isolated. Two of these clones were sequenced in both directions, and 10
additional clones were partially sequenced. Sequence analysis of these
clones revealed identical sequences. The 1.9-kb full-length cDNA has an
open reading frame of 466 amino acid residues and possesses 85%
homology with the human MATK (Fig. 2). A 1.9-kb Matk transcript was detected in murine brain and megakaryocytes using
the mouse Matk cDNA as a probe (data not shown). RNase
protection assay demonstrated only one protected fragment using the
mouse Matk cDNA and RNA isolated from mouse megakaryocytes as
a template (data not shown).
Figure 1:
Southern blot analysis of human genomic
DNA using 5`- or 3`-specific fragment of human MATK cDNA as probes.
Aliquots of 10 µg of HindIII, EcoRI, BamHI, or XbaI digested human genomic DNA were
separated on 1% agarose gel and transferred. Molecular sizes (kb) as determined by migration of
-HindIII
fragments are shown.
Figure 2:
Alignment of the predicted amino acid
sequences (single-letter code) of the mouse Matk and human
MATK gene translated products. Amino acid residues found to be observed
between mouse Matk and human MATK are
boxed.
Chromosomal Localization of the Murine Matk
Gene
Chromosomal localization of Matk in the
mouse-Southern blots of C57BL/6J and M. spretus DNAs
were digested with 29 different restriction enzymes and probed with a
mouse Matk 1.8-kb cDNA. A HincII restriction fragment
length polymorphism (RFLP) was detected (Fig. 3A). The
alleles for this HincII RFLP consists of a 16.5 kb band,
characteristic of C57BL/6J and a 9.7 kb band which is found in M. spretus. These alleles were characterized in 94
DNAs from the C57BL/6J X M. spretus backcross panel.
Results of the haplotype analysis from this mapping data indicate that
the Matk gene co-localizes with D10Mit22 (MIT
anonymous DNA fragment 22) and is linked to Iapls3-28 (intra-cisternal A particle LTR sequence 3-28) on mouse
chromosome 10 (Fig. 3B). The Matk locus mapped
between Iapls3-28 and D10Mit65 (MIT anonymous
DNA fragment 65) and the calculated distances are: Iapls3-28-3.2 ± 1.8
cM-Matk-6.4 ± 3.5
cM-D10Mit65.
Figure 3:
Matk
maps to chromosome 10 in mouse using a C57BL/6J X M. spretus backcross. A, HincII restriction enzyme pattern
for C57BL/6J (B) and for (C57BL/6J X M. spretus) F
heterozygote (BS) genomic DNAs
probed with Matk cDNA. The major difference between the two
DNAs and molecular sizes of fragments in kb are indicated. B,
haplotype analysis of molecular markers in backcross progeny.
Inheritance of chromosome 10 markers in backcross mice from a C57BL/6J
X M. spretus backcross showing linkage and relative
position of Matk. Gene names and references to these loci can
be found in GBASE. The first two columns indicate the number of
backcross progeny with no recombinations. The following columns
indicate recombinational events between adjacent loci (signified by a
change from an open box to a closed box). The number
of recombinants are listed below each column and crossing-over
percentage between adjacent loci is
indicated.
Cloning, Sequence Analysis, Genomic Organization, and
Chromosomal Localization of the Human MATK Gene
We previously
observed that expression of human MATK mRNA in megakaryocytes and brain
was specific and abundant(23) . To determine the exon-intron
organization of the human MATK gene and to identify the potential
tissue-specific response elements, we screened approximately 6
10
total recombinants from a human liver genomic library in
-EMBL-3 for genomic clones under conditions of high stringency
with the 686-bp
P-labeled 3`-gene-specific fragment (HindIII
3`) of the human MATK cDNA (Fig. 4). We
isolated a 15-kb genomic DNA clone, termed
-HG-matk-1. In
addition, using probes derived from both the 3`-end and the 5`-end,
respectively, of the human MATK cDNA (686-bp HindIII
3`-fragment; 639-bp 5`
BgIII fragment), we isolated an
additional two genomic DNA clones of 18-kb genomic DNA clone (termed
-HG-matk-2), and 15-kb genomic DNA clones (termed
HG-matk-3).
Figure 4:
Restriction map and exon/intron
organization of the human MATK gene. BI, BgII, D, H, K, N, PsI, PvII, and S refer to the sites within the human MATK
gene that are susceptible to BalI, BglII, DdeI, HindIII, KPNI, NarI, PstI, PvuII, SmaI, respectively. The 13 boxes indicate the 13 exons. The dotted, shaded, and striped areas within exons 4-7 correspond to the SH3 and SH2
domains and the putative ATP-binding site, respectively. The arrows indicate the region of genomic clones
-HG-matk-2 which were
sequenced.
A restriction map of each genomic clone was constructed by digesting
the phage DNA with a panel of restriction enzymes separately or in
various combinations: SalI, BglII, HindIII, XbaI, and EcoRI. The DNA blots were probed under
conditions of high stringency with either the 5`
BglII
fragment, the BglII
HindIII fragment, or the HindIII
3`-fragment of the human MATK cDNA. In
parallel, a blot was prepared of human liver DNA that had been digested
with the same panel of restriction enzymes. When this DNA blot was
probed with the 686-bp HindIII
3`-gene-specific
fragment or the 639-bp 5`
BglII gene-specific fragment
of the human MATK cDNA, the pattern of hybridization was identical to
that obtained with
-HG-matk-2 (data not shown), indicating that
this clone probably contained the entire gene that encodes human MATK.
The restriction enzyme map of the human MATK gene was constructed, and
the nucleotide sequences of
-HG-matk-1,
-HG-matk-2, and
-HG-matk-3 were determined according to the strategy depicted in Fig. 4. Based on the nucleotide sequences of the genomic
fragments analyzed, two oligonucleotides of 21 nucleotides in length
were synthesized and used as primers to determine the contiguous
nucleotide sequence of the next 200-250 nucleotides in each
direction of the double-stranded DNA. No mismatches were found between
the genomic sequence shown in Fig. 5and the cDNA. The
exon-intron organization and the putative promoter region of the human
MATK gene were determined by this approach.
Figure 5:
Nucleotide and deduced amino acid sequence
of the human MATK gene. The nucleotides are numbered relative to the
putative transcription initiation site. The amino acids are numbered
relative to the translation initiation site. Only the sequence of
introns adjacent to splice junctions is shown in lower-case
letters. Putative regulatory elements are underlined and labeled. The nucleotide sequence of the 5`-flanking region,
the exon/intron junction, and the 13 exons are depicted. The arrow indicates the putative transcription initiation site. The putative
ATP-binding site GXGXXG in exon 7 is underlined. The catalytic domain is boxed in exons
7-13. The SH3 domain and SH2 domain are boxed in exons
4-6. The polyadenylation site in exon 13 is underlined.***
refers to stop codon.
Based on the nucleotide
sequences of its
8.0- and
4.0-kb subcloned fragments, the
human MATK gene is comprised of 13 exons that span about 8 kb of DNA (Fig. 5). The gene is approximately 8 kb from the putative
transcription initiation site to the end of exon 13. Our genomic
-HG-matk-2 clone contained an additional 6 kb of 5`-flanking
sequences and 4 kb of sequences downstream of exon 13. Exon 1 contained
the 5`-untranslated sequence, and exon 2 contained the putative
translation initiation site. The sequence encoding the SH3 domain was
localized on exon 4, while the sequence encoding the SH2 domain was
localized on exons 5 and 6. The putative ATP-binding site
(GXGXXG) (46) was localized on exon 7, and
the entire catalytic domain was localized on exons 7-13. The
intron splice junctions were sequenced for each exon, and an additional
369 bp of 5`-flanking sequence was characterized. The sequence -1
to -270 bp was highly rich in GC content.
The putative
transcription initiation site was identified by primer extension
analysis. A single-stranded DNA that corresponded to the antisense
nucleotide sequence of MATK cDNA (nucleotide residue +1 to
+36) was used in the primer extension reaction with RNA prepared
from CMK cells as the template. About 190 nucleotides were extended
onto the primer resulting in a DNA product of
220 nucleotides in
length (Fig. 6). Therefore, the putative transcription
initiation site is
360 nucleotides upstream of the translation
initiation site. Interestingly, a highly GC-rich region is located just
upstream to the putative transcription initiation site. Additional
primer extension experiments with a different antisense nucleotide
sequence were performed to confirm the putative transcription
initiation site of the human MATK gene (data not shown).
Figure 6:
Determination of the 5`-end of the mRNA
which encodes MATK by primer extension. The primer extension reaction
was performed using control TPA301 RNA (lane 1) and CMK RNA (lane 2). The radiolabeled DNA HinfI fragment (as
well as their size) which are generated by
174-
P-5`-end-labeled are indicated in the left lane (M). The arrow indicates the size of the
oligonucleotide that is polymerized onto the
primer.
The region
upstream of the putative transcriptional initiation site was sequenced
to identify potential cis-acting elements which might be involved in
the regulation of MATK gene expression. Analysis of DNA sequences 369
bp proximal to the putative transcription initiation site revealed
several potential cis-acting elements proximal to the putative promoter
region (Fig. 5). Computer analyses of the putative promoter
region did not identify a classical TATA box. A highly GC-rich region
was found close to the beginning of exon 1, a feature typical for a
selected group of genes lacking a classical TATA
box(33, 47) . Potential cis-acting regulatory
sequences were identified as GATA-1, ``GC box,'' Sp1, APRE,
and APRE1 (see Fig. 5for details). Hamster, human, and mouse
DNAs were digested with BamHI, HindIII, and PstI to identify specific RFLP patterns for each species. A
unique PstI RFLP for MATK was identified in human DNA from the
parental cell lines used to prepare human/rodent cell hybrids (Fig. 7). DNAs from the parental and the somatic hybrid cell
lines were digested with PstI, Southern blotted, and probed.
Analysis indicated that the human-specific PstI pattern was
observed only in cell line 19 which contains human chromosome 19 (Fig. 7).
Figure 7:
Mapping of human MATK to Chromosome 19. PstI-digested genomic DNAs from hamster (h), human (H), and mouse (M) as well as 24 human/rodent somatic
cell hybrids (labeled 1-22, X, and Y)
probed with MATK cDNA. The human-specific RFLP is indicated with arrowheads and is seen in the human control lane and lane
19.
Degradation of MATK mRNA by Antisense
Oligonucleotides
To address the role of MATK in
megakaryocytopoiesis, we exposed purified CD34
cells
to antisense oligonucleotides. We first assessed the stability of MATK
transcripts and the half-life of the protein by exposing CMK cells to
actinomycin D (5 ng/ml) for 15, 30, or 60 min. MATK mRNA was stable for
about 30 min after actinomycin D addition and then destabilized. No
MATK protein was observed after treatment with actinomycin D after 8 h
as determined by Western blot analysis (data not shown).Using these
kinetics, we then incubated CD34
cells in serum-free
medium containing growth factors and modified sense, antisense, or
scrambled oligonucleotides. Equal numbers of cells (1
10
cells) were used for total RNA extraction and subsequent PCR
analysis as described(24) . The remaining cells were seeded in
cultures to assess the biologic effects of oligonucleotide treatment.
The MATK antisense encompassing the second amino acid to the eighth
amino acid resulted in a significant decrease in MATK mRNA levels while
the sense oligonucleotide had no effect (Fig. 8A).
Controls for efficient reverse transcription and mRNA stability were
performed by amplification of actin and c-kit transcripts. These
results indicated that MATK antisense oligonucleotides bound
specifically to MATK mRNA, resulting in its degradation. Furthermore,
no expression of MATK protein was observed in CD34
cells treated with MATK antisense oligonucleotides, while there
was no effect on MATK protein expression in CD34
untreated or treated with sense or scrambled oligonucleotides (Fig. 8B).
Figure 8:
A,
expression of MATK mRNA after treatment of CD34
cells
to sense, antisense, or scrambled antisense oligonucleotides.
CD34
cells from bone marrow were isolated and treated
with other respective oligonucleotides as described under
``Experimental Procedures.'' RNA was extracted and analyzed
for MATK, c-kit, and actin transcripts as described. Autoradiographs
were exposed for 18 h at -80 °C. B, expression of
MATK protein after treatment of CD34
cells to sense,
antisense, or scrambled antisense oligonucleotides. CD34
cells were treated with oligonucleotides as described under
``Experimental Procedures.'' Total lysates were prepared and
products were analyzed by SDS-polyacrylamide gel electrophoresis. MATK
p60 protein was analyzed by Western blot using anti-MATK antiserum
(dilution 1:100).
Effect of MATK Antisense Oligonucleotides on in Vitro
Megakaryocytopoiesis
The proliferation of the megakaryocytic
cell line, CMK, in the presence of MATK antisense and sense
oligonucleotides, was assayed by [
H]thymidine
incorporation and cell viability. This approach has been successfully
used to address the function of regulatory genes such as
c-myb, growth factors such as interleukin-11, and the putative
cytokine receptor c-mpl in
hematopoiesis(24, 48, 49) . A myb antisense
oligonucleotide (5`-GTG CCG GGG TCT TCG GGC -3`) served as a positive
control due to its known inhibitory effects on generation of
megakaryocyte colonies (CFU-MK)(49) . HeLa cells served as
negative controls which do not express MATK. Kinetic and dose-response
studies using the oligonucleotides were performed to determine the
optimal conditions to assess their effects on megakaryocyte growth and
proliferation using CMK cells as a model system. These studies
indicated that the optimal concentration of antisense oligonucleotide
was 70 µg/ml added for 48 h. The sense or antisense
oligonucleotides (70 µg/ml) were then added to the cultures of the
human megakaryocytic cell line CMK. These experiments indicated that
the MATK antisense oligonucleotides inhibited proliferation of CMK
cells to a similar degree (about 50%) as the myb antisense construct.
No effects on HeLa cell growth were noted (Table 1).
To
further address the role of MATK in the regulation of
megakaryocytopoiesis in a more physiological model system, we exposed
purified bone marrow CD34
cells to MATK antisense and
sense oligonucleotides. The CD34
cells were isolated
using immunomagnetic beads as described(24) . CD34
cells were incubated at a concentration of 1
10
cells/ml in serum-deprived medium containing growth factors and
synthetic sense or antisense oligonucleotides. 1
10
cells were used for total RNA extraction and subsequent PCR
analysis while the remaining cells were seeded in plasma-clot cultures
to test the effects of sense/antisense oligonucleotide treatment on
CFU-MK. The generation of megakaryocyte colonies (CFU-MK) from
CD34
progenitor cells treated with MATK antisense was
reduced significantly (about 50%) compared to the sense-treated
CD34
and control untreated cells (Table 1).
These results indicate that MATK antisense oligonucleotides
specifically inhibited in vitro megakaryocytopoiesis using
primary marrow progenitor cells.
Phosphorylation of p60
by MATK
and Csk
p60
protein was incubated
with 1 µM[
-
P]ATP and 3 nM MnCl
in the absence or presence of MATK p60 or Csk
p50, subjected to SDS-PAGE, and then located by autoradiography. As
shown in Fig. 9, p60
was
phosphorylated by MATK or Csk in a time-dependent manner. The degree of
p60
phosphorylation by MATK was similar to
that by Csk. MATK was capable of phosphorylating a synthetic peptide
corresponding to the last 25 amino acid residues, indicating that MATK
phosphorylates Src at carboxyl-terminal tyrosine residues (data not
shown).
Figure 9:
Phosphorylation of p60
by
MATK and Csk. MATK p60 and Csk p50 were immunoprecipitated with
specific antibodies as described under ``Experimental
Procedures.'' Purified p60
(2
units) were incubated with or without immunoprecipitates of MATK and
Csk in a reaction system containing 1 µM [
-
P]ATP and 3 mM MnCl
. Samples were taken at the indicated times and
subjected to SDS-PAGE followed by autoradiography. The labeled protein
was then excised from the gel, and its radioactivity was counted in
scintillation fluid.
To exclude the possibility that the apparent action of MATK
was mediated by enhancement of the autophosphorylating activity of
p60
, we examined whether MATK phosphorylated
p60
without kinase activity. For this,
p60
was treated with an ATP analogue, FSBA,
which is known to inactivate p60
by reacting
with lysine 295(20) . Almost all the kinase activity of
p60
was destroyed by incubation with 1.0
mM FSBA for 60 min at 30 °C. Residual FSBA was quenched by
-mercaptoethanol. The inactivated p60
was then incubated with or without MATK, the degree of
phosphorylation was analyzed by SDS-PAGE as described above, and the
radioactivity in the phosphoprotein corresponding to
p60
was counted (Table 2, Fig. 10). The results showed that MATK phosphorylated the
inactivated p60
. These studies indicate that
MATK indeed catalyzed the phosphorylation of a tyrosine residue on
c-src distinct from the autophosphorylation site.
Figure 10:
Phosphorylation of FSBA-treated
p60
by MATK. p60
or
FSBA-treated p60
were incubated
with or without MATK in a reaction mixture as described in Table 2. Samples were subjected to SDS-PAGE followed by
autoradiography.
Phosphorylation of
p60
by MATK or Csk resulted in a decrease in
their abilities to phosphorylate enolase. The effects were apparent
when activities were measured in the presence of a limited (1
µM) and an excess (10 µM) amount of ATP (data
not shown).
DISCUSSION
In this study we have characterized the human MATK gene,
cloned the murine Matk cDNA, and performed functional studies
of its translated product. Comparison of the deduced amino acid
sequences of human MATK and murine Matk cDNAs revealed 85%
homology, indicating that MATK is highly conserved in human and mouse (Fig. 2). Somatic cell hybrid analysis indicated that human MATK
gene is localized on chromosome 19 while the murine Matk gene
is localized on chromosome 10 within a region which is homologous to
human chromosome 19 (Fig. 3, and 7).
While this article was
in preparation, molecular cloning of murine Ntk from mice fetal thymus (50) and Ctk from mice adult brain (51) were reported.
Sequence analysis of murine Matk revealed >99% homology
with Ctk (differences in amino acids 105 and 106 due to shifting of G
and C nucleotides in this position) and 100% homology with Ntk,
indicating that the reported cDNA Ctk or Ntk represent the murine
homolog of human MATK cDNA. The reported mouse Ntk cDNA (50) has an extra coding region of 41 amino acids like human
MATK cDNA including the translation initiation site in the same
position. The sequence upstream of the translation initiation site of
mouse Ntk is different from the sequence upstream of the translation
initiation site of mouse Matk and Ctk and is probably due to
different exon usage (52) and tissue-specific selection of the
transcription initiation site and the translation initiation site,
suggesting tissue-specific regulation of mouse Matk gene.
Additional findings support the conclusion that mouse Matk,
Ctk, and Ntk are the murine homologs of human MATK. Southern blot
analysis of human and mouse genomic DNA digested with several enzymes
and hybridized with cDNA fragments from the 5`- or 3`-region of human
MATK cDNA, revealed hybridization to a single band (Fig. 1). In
RNase protection assays using mouse brain mRNA as a template, full
protection was demonstrated (data not shown). Matk in the
mouse was mapped to chromosome 10 in a region which is homologous to
human chromosome 19(53) . The Matk gene co-localized
with D10Mit22 which is 1 cM proximal to the Amh gene
(anti-Muellerian Hormone). This region of mouse chromosome 10 also has
some homology to human chromosome 21(53) . We have also mapped
the human MATK gene by using DNAs from human/rodent somatic cell hybrid
lines to human chromosome 19 (Fig. 7). Our results indicated the
exact localization of MATK was chromosome 19 p13.3 based on human-mouse
chromosomal homology and is in full agreement with the reported (54) assignment of the HYL locus determined by fluorescent in situ hybridization.
To determine the underlying
molecular mechanisms of MATK regulation, we cloned, sequenced, and
analyzed the genomic structure of the human MATK gene. This gene
consists of 13 exons which span a genomic distance of about 8 kb
compared with genomic loci of the coding region of Csk (55) and
of Src (56, 57, 58) spanning genomic distance
of 4.9 kb (exons 2-12) and 15 kb (exons 2-12),
respectively. The structure of exon-intron junctions is in agreement
with established consensus sequences(59) . The first exon
encodes the 5`-untranslated region. The second exon encodes the
following 24 amino acid sequence that contains the NH
terminus of the MATK protein. Comparing the genomic structure of
MATK shows similarity with the exon-intron organization of Csk (55) suggesting that the MATK intron-exon structure is
intermediate between the Src-family (56, 57, 58) and the fes/fer group(60, 61, 62, 63) . This
homology is in agreement with the localization of the MATK gene in a
phylogenetic tree close to the Csk gene based on sequence homology
within the catalytic domain as suggested by Brauninger et al.(55) for the Csk gene.
Primer extension reactions were
performed and revealed that
360 bp upstream of the translation
initiation site is the putative transcription initiation site in the
MATK gene. The human MATK gene does not contain a classical TATA box. A
GC-rich region was found upstream of the putative transcription
initiation site. These GC-rich motifs, which could serve as Sp1 sites,
were identified in the putative MATK promoter in close vicinity to the
putative transcription initiation site.
A number of nucleotide
sequences that correspond to known cis-acting elements that enhance or
suppress transcription of other genes were identified in the 396-bp
sequence upstream of the transcription initiation site, including
GATA-1, APRE, several Sp1 sites, and APRE1 (64) . However, it
remains to be determined if these motifs play a functional role in the
regulation of transcription of MATK in megakaryocytes, CD34
marrow cells, or brain.
Recently, molecular cloning of the
human intracellular protein tyrosine kinase (HYL) cDNA was
reported(54) , which appears to be identical to human MATK
cDNA. Sequence analysis of the human MATK gene is in complete agreement
with the human MATK and HYL cDNA sequences. Furthermore, the human MATK
gene is located on human chromosome 19 (Fig. 7), which is the
same chromosomal localization as reported for the HYL
gene(54) . Using 5`-gene-specific and 3`-gene-specific probes
for the human MATK gene, a single band was identified by Southern blot
analysis of human and mouse genomic DNA (Fig. 1). In addition,
RNase protection analysis using the above antisense RNA probes with
mRNA from PMA-treated CMK cells as a template, only one band fully
protected was demonstrated (data not shown). Taken together, these
results indicate that MATK and HYL are the same gene.
High levels of
p60
are found in terminally differentiated
cells such as
platelets(65, 66, 67, 68, 69, 70) ,
suggesting a role in normal cell function that is not related to cell
proliferation. Since the regulation of c-src activation is important in
platelet function, and since MATK shares homology with Csk, we studied
whether MATK could serve as a regulator of p60
in megakaryocytes, the precursors to platelets. Our prior studies
provided evidence that suggested a potential physiologic function of
MATK, based on its restricted expression in CD34
marrow cells and megakaryocytes. MATK expression appeared to be
up-regulated during PMA stimulation, suggesting that MATK could
participate in the process of megakaryocyte maturation and/or platelet
production. The results presented here demonstrate that
p60
in megakaryocytes can be regulated
negatively by MATK. In our reaction system, MATK could phosphorylate
p60
. These results are similar to the
reported effects of Csk and Ctk/Ntk on p60
which appear to phosphorylate the COOH
terminus(50, 51) . Taken together, our data suggest
MATK may act to modulate Src activity in cells of megakaryocytic
lineage.
To further determine whether MATK might play a role in the
regulation of megakaryocytopoiesis, we used an antisense approach.
Exposure of CD34
marrow cells to MATK antisense
oligonucleotides resulted in significant inhibition of megakaryocyte
progenitor formation in vitro. These results indicate that the
MATK-encoded protein likely transduces signals for survival,
proliferation, and/or maturation in megakaryocyte progenitors.
FOOTNOTES
- *
- This work was supported in part by National
Institutes of Health Grants R01 HL51456 and R01 HL46668. The costs of
publication of this article were defrayed in part by the payment of
page charges. This article must therefore by hereby marked
``advertisement'' in accordance with 18 U.S.C.
Section 1734 solely to indicate this fact.
- §
- To whom correspondence should be addressed:
Div. of Hematology/Oncology, New England Deaconess Hospital, One
Deaconess Rd., Boston, MA 02215. Tel.: 617-632-0119; Fax: 617-424-6237.
- (
) - The abbreviations used are: MATK,
megakaryocyte-associated tyrosine kinase; PTK, protein tyrosine kinase;
SH, Src homology; PCR, polymerase chain reaction; PPP, platelet-poor
plasma; P/S, penicillin/streptomycin; PMA, phorbol 12-myristate
13-acetate; GpIIIa, glycoprotein IIIa; RFLP, restriction fragment
length polymorphism; bp, base pair(s); kb, kilobase(s); PAGE,
polyacrylamide gel electrophoresis; FSBA,
5-(p-fluorosulfonylbenzoyl) adenosine.
ACKNOWLEDGEMENTS
We thank Dr. Jerome E. Groopman for critical reading
of the manuscript and very helpful discussion. We thank Dr. Andre
Veillette, McGill University, Montreal, Canada for supplying Csk
antibodies, Dr. Stuart Orkin, Children's Hospital, Harvard
Medical School, Boston, MA for supplying
-EMBL 3 human genomic
library, and Linda Pasztor for valuable discussions on human gene
mapping. We also thank Lucy Rowe, Joe Nadeau, and Ed Birkenmeier of The
Jackson Laboratory for supplying the DNA panel and for performing
analysis of linkage data and Laura Gatson for her technical assistance.
We thank Patricia DeLapp for her help in preparing the manuscript.
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