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-N-Dimethylarginine Dimethylaminohydrolase Homologue, Are Found in a 30-kb Segment of the MHC Class III Region1 ,2
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Medical Research Council Immunochemistry Unit, Department of Biochemistry, Oxford University, Oxford, United Kingdom; and
HGMP Resource Centre, Hinxton, Cambridge, United Kingdom
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Abstract |
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 Top Abstract IntroductionMaterials and MethodsResultsDiscussionReferences |
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,N-dimethylarginine
dimethylaminohydrolase, which is thought to be involved in regulating
nitric oxide synthesis. In addition, three microsatellite markers,
9N-1, 82-2, and D6S273 are contained within the sequence, the last two
of which have been reported to be strongly associated with the
autoimmune disease ankylosing spondylitis. |
Introduction |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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Chromosome mapping studies using somatic cell hybrids, recombinant inbred mouse lines, and in situ hybridization have revealed that all members of the mouse Ly-6 multigene family occupy a single genetic locus on chromosome 15 that is closely linked to the sis and myc proto-oncogenes and to loci that mediate susceptibility to radiation-induced lymphoid malignancy (9, 10, 11). The physical map spans 630 kb and contains at least 18 distinct Ly-6-related sequences (12). Six expressed Ly-6 mouse genes are known (Ly-6A/E, -B, -C, and –G; TSA-1/Sca-2; and ThB) and a seventh, Ly-6F, has been identified at the molecular level (3, 7, 13, 14, 15, 16, 17, 18). The sequences of the leader peptide and membrane-anchoring portions show high similarities, but the sequences of the middle segments apart from the invariant cysteine residues are much more variable. The middle segments probably play an important role in the functional diversity that may distinguish the Ly-6 gene products. To date, three human members of this family, E48 (homologue of mouse ThB), TSA-1/Sca-2 (homologue of mouse TSA-1), and GML, have been mapped in chromosome 8 (8q24-qter region) (19, 20, 21), which is syntenic to mouse chromosome 15. There are other Ly-6-related molecules with diverse functions, such as the three domain urokinase plasminogen activator receptor (uPAR) or CD87, and CD59 (complement protein-blocking assembly of the membrane attack complex) that exhibit a low degree of sequence identity and are encoded by genes that are not in close linkage with any of the Ly-6 family. No human homologue of the Ly-6 gene cluster has been identified to date. Attempts to do so have been hampered by an apparently rapid divergence of the genes between species that has prevented detectable cross-hybridization of Ly-6-like genes much beyond a subset of the rodentia.
We report here sequence analysis of a cosmid (cosEL3) from the human
MHC class III region that has revealed the presence of a cluster of
three Ly-6 superfamily members. MHC occupies a segment of approximately
4 Mbp on the short arm of chromosome 6 (6p21.3) and contains the highly
polymorphic class I and class II genes (22). These genes are
responsible for coding polymorphic cell surface proteins involved in
the presentation and recognition of foreign Ags during immune responses
(23, 24, 25). In man, these two gene clusters are separated by about 1100
kb of DNA termed the class III region (26, 27), which contains a number
of unrelated genes, including those encoding the complement proteins
C2, factor B, and C4 (28); the related cytokines TNF and
lymphotoxin-
/ß (26, 27, 29); and three genes encoding members of
the major heat shock protein (hsp70) family (30, 31).
Susceptibilities to a wide range of diseases have been linked to the MHC. These include Behçet disease, systemic lupus erythematosus, orchitis, celiac disease, insulin-dependent diabetes mellitus, rheumatoid arthritis (RA) and ankylosing spondylitis (AS) (32, 33, 34, 35, 36, 37, 38, 39, 40, 41). Although many disease susceptibilities appear to be due to allelic differences in the class I and class II Ags, some additional loci within the central class III region may contribute to disease susceptibility as well.
In addition to the three new members of the Ly-6 superfamily the cosmid
was found to contain a gene (G6B) encoding a putative new member of the
Ig superfamily and two other genes. The G6 gene encodes a regulatory
molecule of a nuclear channel protein described by Valenzuela et al.
(42), while the G6a gene encodes a putative homologue of the human
enzyme
N,N-dimethylarginine
dimethylaminohydrolase (DDAH) first described in rat kidney by Kimoto
et al. (43). This important enzyme may regulate the
L-arginine-NO pathway by governing the
degradation of endogenous inhibitors of NO synthases (43, 44). In
addition, the cosmid was found to contain the microsatellite markers
D6S273 and 82-2. In a genome-wide screen for susceptibility loci in AS,
the data obtained by Brown et al. (45) clearly indicated that these
two markers, which achieved the highest LOD scores of all
markers tested, were strongly associated with susceptibility to the
disease.
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Materials and Methods |
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The EL3 cosmid clones were sequenced using an M13 shotgun strategy (46) with fluorescent dye primer and dye terminator sequencing chemistries (Amersham, Arlington Heights, IL). Cosmid DNA was sonicated, and fragments from 1–1.5 kb were selected for cloning into M13 mp18. Recombinant M13 mp18 phage DNA was purified from culture supernatants using a Vistra DNA Labstation and was cycle sequenced using ThermoSequenase (Amersham) in a 96-well format on a Hybaid Omnigene thermocycler (Middlesex, U.K.; 95°C for 5 min followed by 20 cycles of 95°C for 30 s and 60°C for 30 s) in the presence of the fluorescent dye-labeled M13 universal primer (5'-TGACCGGCAGCAAAATG-3'). The sequencing reactions were run on an Applied Biosystems 377 automated DNA sequencer (Foster City, CA), and sequence data were analyzed with the Applied Biosystems 377-dedicated software. Individual sequence traces were processed and reassembled using the programs PREGAP and GAP v4.0-ß4 from the Staden suite of software (Medical Research Council Laboratory of Molecular Biology, Cambridge, UK).
Ambiguities within the sequence were resolved, and the sequences across areas of single orientation read were confirmed with dye terminator sequencing chemistries, while gaps between contigs were closed by either sequencing the reverse strand of long clones (>800 nt) that extended into the gap or by sequencing of PCR products covering the gaps.
Transcript profiling
The expression of transcripts was investigated in the cell lines
Jurkat 6 and Molt 4 (T cell), Raji (B cell), HL60 (monocyte), U937
(monocyte), HepG2 (hepatocyte), HeLa (epithelial), HT1080 (epithelial),
and SW620 (adenocarcinoma) with RT-PCR using total RNA and the Promega
RT system, according to the manufacturer’s protocol (gene-specific
primers are shown in Table I
). PCR
primers were designed to give products containing more than one exon so
that amplification products arising from genomic DNA contamination were
easily discernible. The first-round cDNA synthesis was performed in a
final volume of 20 µl with 1 µg of total RNA; 5 µl of this
reaction mix was used per 25 µl of PCR reaction using the
transcript-specific primers and amplification conditions listed in
Table I. Each transcript-specific RT-PCR reaction was performed in at
least triplicate to allow for any variation between reactions. Control
amplification reactions with primers derived from ß-actin were
conducted for each first-round cDNA synthesis reaction. The identities
of PCR products were confirmed by direct dye terminator sequencing.
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The Wisconsin Package version 9-UNIX (GCG), maintained at the University of Oxford Molecular Biology Data Center, was used for the majority of the sequence analysis and database interrogation. The DNA sequence generated was screened against the EMBL, SwissProt, PDB, EMBL-EST, and TIGR-EST (search@hcd.tigr.org) databases to position known genes and identify possible new coding regions. Repetitive elements were identified with the aid of the Repeat Masker server (A. F. A. Smit and P. Green, RepeatMasker at http://ftp.genome.washington.edu/RH/RepeatMasker.html), and potential coding regions were defined using the NIX exon prediction program (http://www.hgmp.mrc.ac.uk/registered/Webapp/nix/) at the HGMP Resource Center, Hinxton (Cambridge, U.K.). Predictions of protein secondary structure, solvent accessibility, and transmembrane regions were conducted using the Jpred-consensus secondary structure prediction server (http://circinus.ebi.ac.uk:8081/) or PredictProtein program (phd@EMBL-Heidelberg.de). The GCG program SIGCLEAVE and the SMART (Simple Modular Architecture Research Tool) server (http://coot.embl-heildelberg.de/SMART) were used to identify leader peptides. Sequence motifs and protein domains were identified using a combination of the GCG program MOTIF, the Prosite Profilescan server (http://µlrec3.unil.ch/software/PFSCAN-form.html), and the SMART server. Multiple alignments of amino acid sequences were performed using Clustalx software, making use of protein structure information from sequences within the PDB database to aid in the alignment wherever possible. Alignments were hand-edited using the GCG9 SeqLab multiple alignment editor.
cDNA selection
Five nanograms of cosmid F9N DNA (overlapping the centromeric
part of EL3), obtained by the alkaline lysis method, was biotinylated
with 16-dUTP (20 µM) and radioactively labeled with
[-32P]dCTP (0.06 µM) using the nick
translation kit from Promega (Madison, WI) (47). A fetal brain cDNA
library (gift from M. Lovett, Department of Biochemistry, University of
Texas Southwestern Medical Center, TX) was supplied ligated to a
linker, to facilitate amplification using primer
3'-CTCGAGAATTCTGGATCCTC. The reaction was heated to 94°C for 10
min and then subjected to 30 cycles of 45 s at 94°C, 45 s
at 58°C, and then 2 min at 72°C before a final stage at 72°C for
10 min. The PCR products were ethanol precipitated and resuspended in
7.5 µl of distilled water. Two micrograms of the selected cDNA was
mixed with 2 µg of COT-1 DNA and 10 ng of BamHI-digested
Lorist 4 vector in a total volume of 10 µl. This mixture was boiled
for 5 min, 10 µl of warmed 2x cDNA hybridization solution (50%
deionized formamide, 1 M NaCl, 50 mM Tris-HCl (pH 7.4), 0.2% BSA,
0.2% Ficoll 400, 0.2% polyvinylpyrrolidone, 0.1% sodium
pyrophosphate, 10% dextran sulfate, and 0.5% SDS) was added, and the
cDNA sample was preannealed at 65°C for 4 h. The preannealed
starting cDNAs were mixed with denatured template and 2x cDNA
hybridization solution in a final volume of 20 µl. This mixture was
then incubated at 65°C for 50 h. After recovery of the template
and elution of the selected cDNAs, the selected cDNAs were preannealed
and hybridized to the remaining template in the same way as the
starting cDNA. cDNAs were recovered from the hybridization mixes using
streptavidin M-280 beads (Dynal, Great Neck, NY). Ten-microliter beads
were washed in 10 µl of binding buffer (supplied by the manufacturer)
before mixing with the hybridization mix for 15 min. The beads were
then washed twice with 1x SSC/0.1% (w/v) SDS and three times for 15
min in 0.1x SSC/0.1% (w/v) SDS at 65°C to remove nonspecifically
bound cDNAs. The selected cDNAs were eluted with 1 M Tris-HCl (pH
7.5).
The secondary selected cDNA products were amplified with linker primers with adaptors containing dump bases to allow UdG cloning using the Cloneamp kit (Life Technologies, Grand Island, NY). PCR products (50–100 ng) were mixed with 25 ng of prepared pAMP 18 vector in the presence of 1 U of uracil DNA glycosylase in UdG annealing buffer. The ligation products were transformed into competent TG1 cells plated out onto L plates (with ampicillin) at low density, and the cDNA inserts were characterized by either dye primer or dye terminator sequencing using the M13 –21 forward primer.
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Results |
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. The location
of exon coordinates and other sequences, such as polyadenylation
signals, can be found in the EMBL database, submission HSA012008. The
derived amino acid sequences of the five proteins encoded by genes
located in the cosmid are shown in Fig. 2.
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The G6C gene.
Six different human and three mouse ESTs from the EST database aligned
over the G6C genomic region. Only one of six human EST entries (H03135)
matched exactly the G6C gene, while the others are only partial
transcripts containing the last exon (accession nos. H03945, W56634,
R27318, W56597, and R25237). One of three mouse EST entries (W12301) is
almost a complete transcript, while the other two contain only exons 1
and 2 (accession nos. AA93044 and AA500454). The G6C gene spans about 3
kb and contains three exons. RT-PCR analysis using primer sequences
located in exons 2 and 3 has revealed expression of G6C only in the T
cell lines Molt 4 and Jurkat 6 (Fig. 3).
Sequencing of the PCR product has allowed the exon boundaries to be
confirmed.
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). This microsatellite has recently been found to be
strongly associated with susceptibility to AS (45). RT-PCR analysis
using primer sequences located in exons 2 and 3 has revealed that the
G6D transcript is expressed in all the cell lines analyzed (Fig. 3).
Sequencing of the PCR product has allowed confirmation of the exon
boundaries.
The G6E gene.
No EST sequence matching G6E was found in EST database searches.
Although the gene appears to be incomplete, the first two exons encode
the putative signal peptide, and the first 24 aa of the Ly-6 domain
containing the first four cysteines. A stop codon was found at the end
of the second predicted exon, which might indicate that G6E is a
pseudogene. In support of this, G6E was found not to be expressed in
any of the cell lines tested, whether activated or not by IFN-
and
PMA (Fig. 3), even though two different primer pairs were
used.
The G6C/D/E proteins
The G6C and G6D genes encode polypeptides of 125 and 133 aa,
respectively. G6E is an incomplete gene and encodes a partial
polypeptide sequence of only 51 aa. The G6C and G6D polypeptides each
contain a leader peptide, a Ly-6-like domain, a transmembrane region
(type 1a), and sequences that indicate that they could be anchored to
the cell membrane via GPI anchors. Cleavage of the putative signal
peptide and the hydrophobic transmembrane region after the Asn residue
next to the last Cys residue would yield mature proteins of about
79–85 aa in length. Alignment with all protein members of the Ly-6
superfamily is shown in Fig. 4 together
with the predicted secondary structural elements (indicated by arrows
(ß-sheets), cylinder (-helix), and lines (loops)). The percent
similarity and identity between the different members of the Ly-6
family are shown in Table II. G6D lacks
two main cysteines obstructing two different disulfide bonds. This is
rare in the family because the 10 cysteines are vital to maintain the
structure. However, one other member of this family is found to have
two cysteines missing (uPAR1, see alignment in Fig. 4). Phylogenetic
analysis of the Ly-6 alignment is shown in Fig. 5, which reveals that both G6C
and G6D belong to the Ly-6 superfamily, although they are differently
related to mouse Ly-6 proteins.
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The G6B gene, which spans about 2 kb, has been predicted by
several exon prediction programs in reverse orientation to the G6A and
G6C genes and contains six exons tightly packed between two sets of
repetitive elements (Fig. 1). A cDNA selection experiment using fetal
brain cDNA as template identified one clone (3/1B7), which contained
the end of exon 2, exons 3 and 4, and the beginning of exon 5 (48). One
EST entry (accession no. AA699838) was also found containing only the
last exon with the predicted polyadenylation signal. We were unable to
determine any mRNA expression when performing RT-PCR analysis on a
number of cell lines, both unactivated and activated.
The predicted G6B protein has 241 aa and contains several interesting
features corresponding to a putative signal transduction receptor. The
translated sequence immediately downstream from the initiator
methionine codon shows a high proportion of hydrophobic amino acid
residues, characteristic of a posttranslationally cleaved leader
sequence from position 1–18. Exon 2 encodes an external domain with
high similarity to Ig variable domains and contains four cysteines, two
of them in good consensus sequences to interact in a disulfide bond,
while the other two might interact with another molecule and induce
dimerization, a feature common in Ig receptors (49). G6B also contains
two key residues that form a salt bridge, Arg85
in strand D with Asp102 in strand F. Alignment
with some Ig V domains is shown in Fig. 6A (50). The percent
similarity and identity between protein sequences shown in the
alignment are given in Table II. G6B also appears to have two putative
Asn glycosylation sites at amino acid positions 77 (NQTN) and 88
(NTTC).
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B), and two
putative phosphorylated tyrosine motifs (53). One of them seems to have
the consensus sequence for an SH2 binding domain
(Y-hydrophobic-X-hydrophobic: YADL at position 211), and the second
motif Thr-X-Tyr at position 235 is common in mitogen-activated protein
kinases. A schematic representation of the different motifs in G6B is
shown in Fig. 6C. It is likely that G6B might be involved in
some kind of signal transduction events The G6A gene
The G6A gene contains eight exons that span about 3 kb of DNA
(Fig. 1). The 5' untranslated region of the mRNA is encoded in the
first two exons and part of the third (from positions 12,052 to
12,257). When either the first or second exon is used, the splicing of
the third exon changes, and it starts at position 12194. The most
common ESTs (
30 entries in total) correspond to an mRNA starting at
exon 1, although other splice variants are also apparent (accession no.
of ESTs starting at exon 2: H87910, AA133714; accession no. of ESTs
starting at exon 3: AA298342, AA134375, and R11949). The longest open
reading frame from all splice variants starts at position 12,258 in
exon 3 and codes for a 285-aa polypeptide of 31.4 kDa.
Database searches revealed that the putative human polypeptide shared
96.7% identity with the derived amino acid sequence encoded by the
mouse cDNA clone (7u) isolated from a malignant melanoma cDNA library
(54), and 48.75% identity (70.46% similarity) with the rat kidney
enzyme DDAH (43) (EC 3.5.3.18; Fig. 7).
The active center of the enzyme is probably between residues 119 and
166, which are highly conserved (see Fig. 7). Three small motifs common
to the prokaryote enzyme family that catabolize L-arginine
to L-citruline (55) are found in the DDAH family as well
(highlighted in Fig. 7).
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). However, Spanjaard et al. (54) only detected
expression of the mouse mRNA in large intestine, with low levels in
lung and brain. In rat, expression was detected in kidney, pancreas,
liver, brain, lung, and heart (56), and the protein was clearly shown
to exist in peritoneal neutrophils and macrophages (56). Recently, the
DDAH has been characterized in bovine brain tissue, and the protein is
detected in total brain and kidney, at low levels in heart, liver, and
lung, but not in blood, muscle, spleen, or intestine extracts (57). The
PCR product obtained from the RT-PCR experiment has been sequenced, and
the exon boundaries checked. The G6 gene
The gene G6 was originally defined using a 2.4-kb
HindIII genomic fragment lying adjacent to a CpG island,
which hybridized to mRNA species of 1.5 and 1.4 kb in the cell lines
U937, U937 stimulated by PMA, HepG2, and Molt4, and mRNA species of 1.5
and 1.45 kb in the cell line Raji (31). A fragment containing the 5'
untranslated sequence in exon 2 was only detected in one of the mRNA
species (58). Two mRNA species have also been described by Valenzuela
et al. (42) (1.0 and 1.2 kb) that are differently regulated by PMA,
retinoic acid, IFN-, and IL-2. They also detected a difference in
the 5' untranslated region between the two species. The gene spans 6 kb
and contains seven exons (Fig. 1). The microsatellite marker 82-2 which
has been found to be strongly associated with susceptibility to AS
(45), is located between the second and third exons. The longest open
reading frame of G6 starts in exon 2 and codes for a polypeptide of 241
aa with a predicted Mr of 26.9 kDa.
The amino acid sequence is identical with the polypeptide described by
Valenzuela et al. (42), which they claimed could be a putative nuclear
chloride ion channel protein.
Two PEST regions have been found in G6 (wwwserver at JMB Jena). These regions are rich in proline (P), glutamic acid (E), serine (S), and threonine (T) and begin and end with relatively charged residues, but most commonly lysine, arginine, and histidine. Those regions are characteristic of proteins that are rapidly degraded within eukaryotic cells (59). PEST sequences have been reported in a number of proteins that are located in the nucleus, including c-Fos, c-Myc, p53, Bmil, and Upl (59, 60, 61).
Interestingly there are two basic sequences (KRR and KKYR) at positions
49 and 192 in the protein that satisfy the criteria for nuclear
localization signals (62). In support of this, there are four putative
casein kinase II sites near these nuclear localization signals at
positions 44 (TTUD), 174 (TLAD), 198 (TIPE), and 222 (TCPD) (63).
Casein kinase II sites have been located close to many confirmed
nuclear localization signal sequences found in other proteins, and
phosphorylation at these sites has been implicated in the rate of
nuclear transport. Other post-translation modifications that could
occur in G6 are shown in Fig. 2.
No N-terminal signal peptide is found in the G6 protein sequence (PsortII and Nakai server). None of the programs used (Tm prediction, PHD) predicted a good transmembrane region in the protein, suggesting a globular three-dimensional structure for G6.
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Discussion |
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The genes G6C and G6D, and possibly also G6E, encode small Cys-rich proteins of 79–82 aa that appear to be novel members of the Ly-6 family. They are probably anchored in the cell membrane by a C-terminal GPI moiety, a post-translational modification in common with each member of the Ly-6 family described to date. The finding of Ly-6-like proteins in humans is important because of the independent regulation of each member of this family, generating distinct patterns of expression during hemopoiesis and immune responses. This information suggests that they provide distinct functions affecting various stages of leukocyte development. Only a few human genes with this homology have been described to date, the E48 homologue (19) to the mouse ThB gene (64), the Tsa-1/Sca-2 homologue (20) (or 98604 (65) or RIG-E (66)) to the mouse Tsa-1/Sca-2 gene (6), and the GML (21). The E48 (involved in cell-cell adhesion), Tsa-1/Sca-2 (recently, physically and functionally associated with the TCR via CD3 (67)), and GML (the expression of which is induced by p53) genes have been localized in human chromosome 8 (19, 20, 21), which is the syntenic region of mouse chromosome 15, where the mouse Ly-6 gene cluster has been localized (12). No Ly-6 domain has been found in combination with domains of any other superfamily; this may be because the exon structures known for this superfamily are not suited to exon shuffling. The SP-10 (sperm acrosomal protein) is another human member of the Ly-6 superfamily that is encoded by a gene located in chromosome 11q23-q24 (68). However, it contains some unique features that distinguish it from other members of the superfamily, including G6C and G6D. For example, more than half of the original protein sequence is unrelated to Ly-6, being encoded by a completely different exon not present in any other Ly-6 member, and it lacks the GPI anchor, which is a distinctive feature of the Ly-6 Ags.
The G6C, -D, and -E genes are not direct homologues of any of the mouse Ly-6 genes given that the level of sequence identity is only 21.62–27.03%, but being members of the Ly-6 superfamily, they might have similar functions. Taking into account that both genes, G6C and G6D, have different expression patterns in the cell lines tested, an in-depth characterization of these genes will help to define a more accurate functionality.
The G6B gene
G6B is an Ig-like receptor with different signal transduction motifs found in the putative cytoplasmic domain of the molecule. The Ig superfamily is a large group of related proteins that function, mainly in the immune system, in cell-cell recognition or in the structural organization and regulation of muscle (49). The various members of the superfamily are built of homologous domains of approximately 100 residues and with a structure formed by two ß-sheets packed face to face. A disulfide bond is almost always formed by cysteines localized in strands B and F, which are one of the most conserved in the Ig domain. Some of the members have more than two cysteines, and it is believed that this contributes to dimerization. Individual members of the superfamily can differ in the number and size of strands in the two ß-sheets and in the size and conformation of the links between the strands. Similarities in sequences and structures were found, however, and these allow the different members to be grouped into what Williams and Barclay (49) call sets. V set and V-related domains have about 65–75 aa residues between the conserved disulfide bond, and there are four ß-strands in each ß-sheet plus a short ß-strand segment across the top of the domain. G6B is more related to the V set, as it contains 71 aa in between the two cysteines most likely to form the disulfide bond.
Harpaz and Chothia (50) defined a new set called I defined by 20 key amino acid positions that form the characteristic folds of the set. Ig molecules that follow set I seem to be involved in the cell adhesion and cell surface recognition processes. Some of the previous V and C2 sets fall into this new set I. Alignment of G6B with some other variable domains in a manner similar to that used by Harpaz and Chothia highlighted the conservation of 18 of the 20 key sites in G6B. This alignment is based on a secondary structure prediction that defined the approximate position of all the ß-strands. Other features that indicate an Ig domain are that the majority are encoded within one single exon, which is always phase 1. Both features are found in the predicted variable domain of G6B, providing more evidence for its inclusion in the superfamily. Two residues important for the formation of a salt bridge are also conserved, the arginine residue in strand D with aspartic acid in strand F. Of the four cysteines found in the predicted sequence of G6B, the two in strands B and F most likely form a disulfide bond. One of the other cysteines is localized after the Ig-like domain and before the helical transmembrane region, which could indicate the possible existence of G6B as a dimer, either disulfide linked to itself or to another polypeptide.
Interestingly, the BG genes within the chicken MHC complex have been found to encode molecules composed of a single extracellular domain that resembles an Ig V-type domain, a transmembrane region, and a 217-aa cytoplasmic domain (69). We have compared G6B with the BG molecules and have found that they share 20% identity (26% similarity). Moreover, the intracellular segment of sequence is 3 times larger in the BG molecules compared with G6B, and they share no similarity whatsoever. Thus, although G6B and the BG molecules are members of the Ig superfamily, the lack of sequence similarity indicates that they are unrelated to each other.
One of the internal motifs corresponds to a short proline-rich sequence
of 10 aa that could bind to a SH3 (Src homology 3) domain (70) in a
left-handed PPII helix conformation (a 3-fold symmetry helix, with
proline residues usually in one face). PPII helices in globular
proteins are also ideal mediators of protein-protein interactions since
most of these motifs are located on the surface of their proteins
(71).
G6B also contains two putative phosphorylated tyrosine residues with one of them at least in a consensus sequence for a SH2-binding motif. Thus, G6B contains all the possible features to be a signal transduction receptor.
The G6A gene
The G6A protein is a homologue of the enzyme DDAH that is thought
to regulate the production of NO by metabolizing
N-mono-methyl-L-arginine
and asymmetric dimethyl-L-arginine to
L-citruline, both of them analogues of
L-arginine and direct inhibitors of constitutive
and inducible NO synthases (44, 72). Although G6A is probably not the
human DDAH enzyme itself, it is likely that it could still function in
a similar way as DDAH, but have different specificity. Taking into
account that
N-mono-methyl-L-arginine
has a therapeutic effect in different inflammatory processes (73, 74, 75)
and NO production has been found to contribute to the development of
insulin-dependent diabetes mellitus (76, 77), examination of the exact
function of G6A might add some valuable information to these
processes.
Among all arginine-using or -producing enzymes only the
dimethylargininase and arginine deiminase enzyme families contain
three motifs in common, which are thought to be involved in
functionality or in maintaining their structure (55) (Fig. 7). Both
families catalyze the hydrolysis of L-arginine into
L-citruline, but the arginine deiminase enzyme is found
exclusively in prokaryotes. Interestingly, arginine deiminase is known
to be involved in strongly inhibiting cell growth, suppressing IL-2
production and IL-2R expression, and inducing apoptotic cell death in T
lymphoblasts (78).
The G6 gene
The genomic localization of NCC27 is in the central part of the MHC class III region and corresponds exactly with the gene described in this paper as G6. NCC27 has been demonstrated to be in the nuclear membrane (42). Although the authors describe the protein as a chloride ion channel itself, they do not reject the possibility of NCC27 acting as a regulatory subunit of a multiprotein chloride ion complex. We think that this second hypothesis might be more appropriate due to the presence of several PEST sequences (seven in bovine p64 and two in G6 or NCC27) that could act as signals for the rapid degradation of the protein, and the clear lack of a transmembrane region. Under physiological conditions, nuclear localization must be subject to complicated regulatory mechanisms, since the presence of certain proteins in the nucleus is required only at very specific moments in the cell cycle or only in response to short-lived stimuli.
It is apparent that many of the genes located in the MHC class III region are good candidate genes for susceptibility to diseases such as insulin-dependent diabetes mellitus or AS due to the possibility of their involvement in the immune and/or inflammatory responses. In a recent genome-wide screening for susceptibility loci in AS, markers D6S273 and 82.2, which lie between the second and third exons of G6D and G6, respectively, achieved the highest LOD scores of all markers tested (45). In the case of marker D6S273, the LOD score obtained was 3.8 (p = 1.4 x 10-5), while the strongest linkage was observed with marker 82.2, which achieved a LOD score of 8.1 (p = 1 x 10-9). Given that some of the genes in the immediate vicinity of these markers could have putative immune-related functions, it is tantalizing to speculate that one of them could be a major susceptibility factor in AS. The evidence generated from the EST databases and RT-PCR has also highlighted the complexity of this region, with many of the genes being differently and specifically expressed. Also, the MHC class III region remains among the most gene-dense regions of the human genome with, on the average, one gene per 10 kb of DNA. Indeed, the gene density of the 28.1-kb region discussed here is now one gene per 5.6 kb of DNA.
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Acknowledgments |
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Footnotes |
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2 The nucleotide sequence reported in this paper has been submitted to the EMBL databank with accession number HSA012008.
3 Current address: HGMP Resource Centre, Hinxton, Cambridge, U.K. CB10 1SB.
4 Current address: Department of Biomolecular Sciences, The Mill Building, University of Manchester Institute of Science and Technology, P.O. Box 88, Manchester, U.K. M60 1QD.
5 Address correspondence and reprint requests to Dr. R. Duncan Campbell, HGMP Resourse Centre, Hinxton, Cambridge, CB10 1SB, U.K. E-mail address:
6 Abbreviations used in this paper: Ly-6, leukocyte Ag 6; Tsa-1/Sca-2, thymic shared Ag-1/stem cell Ag-2; ThB, thymocyte B Ag; E48, monoclonal antibody E48; GML, GPI-anchored molecule-like protein; RA, rheumatoid arthritis; AS, ankylosing spondylitis; DDAH, enzyme N,N-dimethylarginine dimethylaminohydrolase; uPAR, urokinase plasminogen activator receptor; SH2–3, Src homology 2–3; ADMA, asymmetric dimethyl-L-arginine; EST, expressed sequence tag.
Received for publication February 2, 1999. Accepted for publication April 14, 1999.
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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-bungarotoxin and other neurotoxins. J. Immunol. 150:5379.[Abstract]
and ß are linked to the major histocompatibility complex. Proc. Natl. Acad. Sci. USA 83:8699.,N-dimethylarginine dimethylaminohydrolase from rat kidney. Biochim. Biophys. Acta 1337:6.[Medline]
,N-dimethylarginine dimethylaminohydrolase in the nitric oxide generating systems of rats using monoclonal Ab. Arch. Biochem. Biophys. 300:657.[Medline]
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