The epithelium of the pharynx contributes to the formation of gills in hemichordates, urochordates, cephalochordates and primitive vertebrates, and is therefore a key structure for understanding developmental mechanisms underlying the establishment of chordate body plans. Pax1- and Pax9-related genes encode transcription factors which are expressed in the pharyngeal region of cephalochordates as well as in the vertebrate pharyngeal pouch epithelium that forms the thymus and parathyroid glands. To explore the molecular basis underlying the occurrence and modifications of the pharyngeal epithelium during evolution, we isolated cDNA clones for Pax1- and Pax9-related genes of urochordates (HrPax1/9 of Halocynthia roretzi and CiPax1/9 of Ciona intestinalis) and a hemichordate (PfPax1/9 of Ptychodera flava) from gill cDNA libraries. Each gene is present as a single copy per haploid genome. All of the cDNAs encode typical paired domains and octapeptides but not a homeodomain, as is also true of other Pax1- and Pax9-related genes. Molecular phylogenetic analysis based on comparison of the paired domain amino-acid sequences suggests that HrPax1/9, CiPax1/9 and PfPax1/9 belong to the Pax1/9 subfamily, and that they are descendants of a single precursor of Pax1/Pax9. Screening of HrPax1/9 cDNA clones yielded six different types of transcripts which were generated by alternative splicing. Northern blot, RT-PCR/Southern and in situ hybridization analyses revealed that HrPax1/9, CiPax1/9 and PfPax1/9 are not expressed during early embryogenesis but are expressed in the epithelia of differentiating gills, suggesting that these genes encode gill-specific transcription factors. The Pax1/9 genes therefore might provide the first developmental genetic corroboration of hypotheses of organ-level homology that unifies hemichordates, urochordates and cephalochordates.

Arenas-Mena
C.
,
Martinez
P.
,
Cameron
R. A.
,
Davidson
E. H.
(
1998
)
Expression of the Hox gene complex in the indirect development of a sea urchin.
Proc. Natl. Acad. Sci. USA
95
,
13062
13067
Bateson
W.
(
1886
)
The ancestry of the Chordata.
Q. J. Microsc. Sci
26
,
535
571
Bopp
D.
,
Jamet
E.
,
Baumgartner
S.
,
Burri
M.
,
Noll
M.
(
1989
)
Isolation of two tissue-specific Drosophila paired box genes, Pox meso and Pox neuro.
EMBO J
8
,
3447
3457
Burri
M.
,
Tromvoukis
Y.
,
Bopp
D.
,
Frigerio
G.
,
Noll
M.
(
1989
)
Conservation of the paired domain in metazoans and its structure in three isolated human genes.
EMBO J
8
,
1183
1190
Chomczynski
P.
,
Sacchi
N.
(
1987
)
Single-step method of RNA isolation by acid quanidinium thiocyanate-phenol-chloroform extraction.
Analyt. Biochem
162
,
156
159
Czerny
T.
,
Bouchard
M.
,
Kozmik
Z.
,
Busslinger
M.
(
1997
)
The characterization of novel Pax genes of the sea urchin and Drosophila reveal an ancient evolutionary origin of the Pax2/5/8 subfamily.
Mech. Dev
67
,
179
192
Dahl
E.
,
Koseki
H.
,
Balling
R.
(
1997
)
Pax genes and organogenesis.
BioEssays
19
,
755
765
Deutsch
U.
,
Dressler
G. R.
,
Gruss
P.
(
1988
)
Pax 1, a member of a paired box homologous murine gene family, is expressed in segmented structures during development.
Cell
53
,
617
625
Di Gregorio
A.
,
Levine
M.
(
1998
)
Ascidian embryogenesis and the origins of the chordate body plan.
Curr. Opin. Genet. Dev
8
,
457
463
Felsenstein
J.
(
1985
)
Confidence limits on phylogenies: an approach using the bootstrap.
Evolution
39
,
783
791
Harada
Y.
,
Yasuo
H.
,
Satoh
N.
(
1995
)
A sea urchin homologue of the chordate Brachyury (T) gene is expressed in the secondary mesenchyme founder cells.
Development
121
,
2747
2754
Higgins
D. J.
,
Bleasby
A. J.
,
Fuchs
R.
(
1992
)
Clustal V: improved software for multiple sequence alignment.
Comput. Appl. Biosci
8
,
189
191
Holland
N. D.
,
Holland
L. Z.
(
1995
)
An amphioxus Pax gene, AmphiPax-1, expressed in embryonic endoderm, but not in mesoderm: implications for the evolution of class I paired box genes.
Mol. Mar. Biol. Biotech
4
,
206
214
Hoshiyama
D.
,
Suga
H.
,
Iwabe
N.
,
Koyanagi
M.
,
Nikoh
N.
,
Kuma
K.
,
Matsuda
F.
,
Honjo
T.
,
Miyata
T.
(
1998
)
Sponge Pax cDNA related to Pax-2/5/8 and ancient gene duplications in the Pax family.
J. Mol. Evol
47
,
640
648
Koseki
H.
,
Wallin
J.
,
Wilting
J.
,
Mizutani
Y.
,
Kispert
A.
,
Ebensperger
C.
,
Herrmann
B. G.
,
Christ
B.
,
Balling
R.
(
1993
)
A role for Pax-1 as a mediator of notochordal signals during the dorsoventral specification of vertebrae.
Development
119
,
649
660
Lowe
C. J.
,
Wray
G. A.
(
1997
)
Radical alterations in the roles of homeobox genes during echinoderm evolution.
Nature
389
,
718
721
Mansouri
A.
,
Stoykova
A.
,
Torres
M.
,
Gruss
P.
(
1996
)
Dysgenesis of cephalic neural crest derivatives in Pax7 /mutant mice.
Development
122
,
831
838
Muller
T. S.
,
Ebensperger
C.
,
Neubuser
A.
,
Koseki
H.
,
Balling
R.
,
Christ
B.
,
Wilting
J.
(
1996
)
Expression of avian Pax1 and Pax9 is intrinsically regulated in the pharyngeal endoderm, but depends on environmental influences in the paraxial mesoderm.
Dev. Biol
178
,
403
417
Neubuser
A.
,
Koseki
H.
,
Balling
R.
(
1995
)
Characterization and developmental expression of Pax9, a paired-box-containing gene related to Pax1.
Dev. Biol
170
,
701
716
Neubuser
A.
,
Peters
H.
,
Balling
R.
,
Martin
G. R.
(
1997
)
Antagonistic interactions between FGF and BMP signaling pathways: a mechanism for positioning the sites of tooth formation.
Cell
90
,
247
255
Nornes
S.
,
Mikkola
I.
,
Krauss
S.
,
Delghandi
M.
,
Perander
M.
,
Johansen
T.
(
1996
)
Zebrafish Pax9 encodes two proteins with distinct C-terminal transactivating domains of different potency negatively regulated by adjacent N-terminal sequences.
J. Biol. Chem
271
,
26914
26923
Ogasawara
M.
,
Satoh
N.
(
1998
)
Isolation and characterization of endostyle-specific genes in the ascidian Ciona intestinalis.
Biol. Bull
195
,
60
69
Peters
H.
,
Doll
U.
,
Niessing
J.
(
1995
)
Differential expression of the chicken Pax-1 and Pax-9 gene: in situ hybridization and immunohistochemical analysis.
Dev. Dyn
203
,
1
16
Peters
H.
,
Neubuser
A.
,
Kratochwil
K.
,
Balling
R.
(
1998
)
Pax9 -deficient mice lack pharyngeal pouch derivatives and teeth and exhibit craniofacial and limb abnormalities.
Genes Dev
12
,
2735
2747
Saitou
N.
,
Nei
M.
(
1987
)
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Mol. Biol. Evol
4
,
406
425
Satoh
N.
,
Jeffery
W. R.
(
1995
)
Chasing tails in ascidians: developmental insights into the origin and evolution of chordates.
Trends Genet
11
,
354
359
Stapleton
P.
,
Weith
A.
,
Urbanek
P.
,
Kozmik
Z.
,
Busslinger
M.
(
1993
)
Chromosomal localization of seven Pax genes and cloning of a novel family member, Pax9.
Nature Genet
3
,
292
304
Strachan
T.
,
Read
A. P.
(
1994
)
PAX genes.
Curr. Opin. Genet. Dev
4
,
427
438
Sun
H.
,
Rodin
A.
,
Zhou
Y.
,
Dickinson
D. P.
,
Harper
D. E.
,
Hewett-Emmett
D.
,
Li
W. H.
(
1997
)
Evolution of paired domains: isolation and sequencing of jellyfish and hydra Pax genes related to Pax-5 and Pax-6.
Proc. Natl. Acad. Sci. USA
94
,
5156
5161
Tagawa
K.
,
Humphreys
T.
,
Satoh
N.
(
1998
)
Novel pattern of Brachyury gene expression in hemichordate embryos.
Mech. Dev
75
,
139
143
Timmons
P. M.
,
Wallin
J.
,
Rigby
P. W.
,
Balling
R.
(
1994
)
Expression and function of Pax 1 during development of the pectoral girdle.
Development
120
,
2773
2785
Turbeville
J. M.
,
Schulz
J. R.
,
Raff
R. A.
(
1994
)
Deuterostome phylogeny and the sister group of the chordates: Evidence from molecules and morphology.
Mol. Biol. Evol
11
,
648
655
Wada
H.
,
Satoh
N.
(
1994
)
Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA.
Proc. Natl. Acad. Sci. USA
91
,
1801
1804
Wada
H.
,
Saiga
H.
,
Satoh
N.
,
Holland
P. W. H.
(
1998
)
Tripartite organization of the ancestral chordate brain and the antiquity of placodes: insights from ascidian Pax-2 / 5 / 8, Hox and Otx genes.
Development
125
,
1113
1122
Wallin
J.
,
Wilting
J.
,
Koseki
H.
,
Fritsch
R.
,
Christ
B.
,
Balling
R.
(
1994
)
The role of Pax-1 in axial skeleton development.
Development
120
,
1109
1121
Wallin
J.
,
Eibel
H.
,
Neubuser
A.
,
Wilting
J.
,
Koseki
H.
,
Balling
R.
(
1996
)
Pax1 is expressed during development of the thymus epithelium and is required for normal T-cell maturation.
Development
122
,
23
30
Yasuo
H.
,
Satoh
N.
(
1993
)
Function of vertebrate T gene.
Nature
364
,
582
583
This content is only available via PDF.