|
|
||||||||
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Minireview |
a Laboratory of Molecular Evolution, Department of Molecular Biosciences, University of Adelaide, South Australia 5005, Australia
| ABSTRACT |
|---|
|
|
|---|
gamete biology
| INTRODUCTION |
|---|
|
|
|---|
By 1994, inconsistent naming of the ZP genes had resulted in a confused system of nomenclature, making communication about the ZP gene family difficult. To overcome this difficulty, Harris et al. [6] proposed a unified system of nomenclature in which ZP genes were named in order of the length of their encoded protein sequence, from longest to shortest. Unfortunately, under these criteria, the mouse ZP genes fall in the order ZP2, then ZP1, and then ZP3. To avoid confusion arising from swapping the names of mouse ZP1 and ZP2, a new letter-based system was introduced. Thus, ZP2 became ZPA, ZP1 became ZPB, and ZP3 became ZPC. Acceptance of the proposed new system of nomenclature has been less than universal, with the number system and the letter system being used concurrently by different groups [9, 10].
The complete cDNA sequence of the mouse ZP1 gene was determined subsequent to the sequence of the human ZPB cDNA sequence [6, 11]. It was assumed that the mouse ZP1 was orthologous to human ZPB (i.e., both genes descended from a single common ancestral gene that diverged at a speciation event), because it shared greater amino acid sequence identity with human ZPB than with human ZPA or ZPC. Even before publication of the chicken and human ZP1 gene sequences [7, 12], phylogenetic analyses suggested that mouse ZP1 and human ZPB were paralogous (i.e., descended from different genes created by a gene duplication). Hughes and Barrett [12] identified a human genomic sequence orthologous to the mouse ZP1 gene and paralogous to the human ZPB gene. Soon after, Bausek et al. [7] published the sequence of a chicken ZP1 gene. Their analysis suggested that a gene duplication, predating the divergence of fish and amphibians, gave rise to two paralogous groups of genes within the ZPB subfamily: ZP1 and ZPB.
Whereas the mammalian ZP has three main glycoprotein components, the egg envelope of Xenopus laevis is comprised of six or more [4]. An orthologue of each of the three groups of mammalian ZP glycoprotein has been found in X. laevis [5, 13, 14]. Two additional X. laevis ZP genes, with no known mammalian orthologues, have also been characterized: ZPAX [15] and ZPA [16]. An additional gene in Oryzias latipes, called ZPA, shares a high level of sequence identity with the X. laevis ZPAX gene. Evolutionary analysis suggested that the Xenopus ZPA gene is an orthologue of the human and pig ZPA genes and that ZPAX evolved from a gene paralogous to the precursor of the ZPA and ZPB genes [15].
The three accepted subfamilies of genes within the ZP gene family each have two names at present: ZPA or ZP2, ZPB or ZP1, and ZPC or ZP3. The difficulties in maintaining this dual nomenclature system have come to a head. It is no longer possible to use ZPB and ZP1 interchangeably to describe the same orthologous set of genes, because a subset of the genes called ZP1 is paralogous to other ZPB (ZP1) genes. In addition to these three subfamilies, two ZP genes from X. laevis and one ZP gene from O. latipes have evolutionary origins that are uncertain. Here, we show the relationships within the ZP gene family in a comprehensive phylogeny based on an analysis of cDNA sequences, and we use the phylogeny to address problems with the current system of nomenclature.
| PHYLOGENETIC ANALYSES |
|---|
|
|
|---|
Sequences included in phylogenetic analyses of the ZP genes are listed in Table 1. This table includes the name for each of the genes as it appears in the GenBank database together with a suggested name based on the phylogenetic relationships established in the present study.
|
Nucleotide sequence alignments of the ZP genes were carried out based on protein sequence alignments using both BioEdit [17] and CLUSTAL W [18] software. Phylogenetic analyses were carried out using the following methods: 1) maximum parsimony with bootstrap; 2) UPGMA (unweighted pair group method with arithmetic mean) using maximum likelihood distances with bootstrap (PHYLIP software [19]); 3) maximum likelihood (PAUP software [20]); 4) likelihood with Markov-chain Monte Carlo (MCMC) sampling (BAMBE software [21]); and 5) quartet puzzling (Puzzle [22]).
Bootstrap analyses were conducted using 1000 pseudoreplicates (parsimony) or 100 pseudoreplicates (maximum likelihood distances) of the data set. Likelihood with MCMC analyses were performed using the likelihood model described by Tamura and Nei [23]. Codon positions were analyzed independently of each other. Nucleotide frequencies and substitution rates were estimated independently for each codon position. Branch swapping was global for both the burn-in and the cycling phase. The rate of convergence of the Markov chain to the posterior distribution was optimized as directed by the authors of the BAMBE program. The consensus tree shown (Fig. 1) was found in three separate runs from random starting points, suggested by Simon and Larget [21] as the minimum requirement for demonstrating sufficient sampling from the posterior probability distribution. Relative rates tests were performed using the program K2wuli [24], which conducts the relative rates test described by Wu and Li [25].
BAMBE Tree
The results of a likelihood analysis with MCMC are shown in Figure 1. A clear hierarchy of relatedness is apparent in the unrooted phylogeny of the ZP genes (Fig. 1). A suggestion for a consistent nomenclature system, based on the hierarchical structure of this phylogeny, is outlined later. At the highest level of the hierarchy lies the gene family, which includes every ZP gene. The gene family can be easily separated into four subfamilies, which are indicated in Figure 1. All the genes of a subfamily are paralogous to all the genes of other subfamilies. The genes in each of the ZPA, ZPB, and ZPC subfamilies can be traced to a single ancestral duplicate gene. The genes of the ZPX subfamily can be traced to two ancestral duplicate genes. Characterization of additional ZPX genes is required to determine if these genes are a single subfamily encompassing two paralogous lineages (like the ZPB subfamily) or two distinct subfamilies. A third level of hierarchy exists within the ZPB subfamily, which has three gene groups: ZPB, ZPB1, and ZPB2. The ZPB group is orthologous to both the ZPB1 and ZPB2 groups, whereas the two latter groups are paralogous, having evolved from different duplicates of an ancestral ZPB gene. It is unfortunate that the probabilities associated with the branching points of the ZPX genes are low. This may be attributed to the duplications that gave rise to both ZPX paralogues and the ZPB and ZPA subfamilies occurring over a short period of evolution, then being reconstructed after a comparatively long period of evolution.
|
Other Methods
The major branches of the maximum parsimony and the maximum likelihood distance trees had an identical topology to the tree shown in Figure 1. The bootstrap values associated with both trees were generally lower than published logical probabilities (data not shown; available on request). Branching orders of the X. laevis ZPX2 (xenopus-ax) and the ZPX1 genes were supported by maximum parsimony bootstrap values of 65% and 52%, respectively. The maximum likelihood distance tree placed the ZPX genes in their illustrated position with a bootstrap of 81% (though the relationships between the individual ZPX genes were unresolved). Quartet puzzling was unable to resolve any of the deep branches of the ZP gene tree.
| EVOLUTIONARY HISTORY |
|---|
|
|
|---|
Almost all ZP genes have a signal peptide at their N-terminus and a trans-membrane domain at their C-terminus. Between these two domains, ZP genes have a conserved region originally characterized in the ZP genes: the ZP domain [26]. No appropriate outgroup exists for use with full-length ZP cDNA sequences, but other known sequences contain ZP domains [26, 27]. When the ZP domain of chicken ß-tectorin was used as an outgroup for phylogenetic analyses of the ZP domains of the ZP genes, the root of the tree consistently lay between the ZPC subfamily and the remainder of the tree. Confidence levels associated with the branching order of the ZP domain trees were lower than those on the full-length tree (Fig. 1), and small changes in the branching order were observed.
Another approach to identifying the most ancient branch of the ZP gene phylogeny required the assumption that the ZP genes evolved in a clock-like manner (i.e., that the rates of nucleotide substitution are approximately equal for the genes being studied). If this assumption holds true within statistical limits and a phylogeny is derived under this assumption, then the deepest branch of this phylogeny should approximate the position of the root of the tree. Relative-rates tests using the method of Wu and Li [25], which requires an outgroup, showed that the assumption of a molecular clock held true across the ZP domain of almost all of the ZP genes (data not shown). Rodent ZPAs, X. laevis ZPC, and the ZPB1 genes were the exceptions. Subsequent UPGMA and BAMBE analyses, for which the molecular clock was assumed, of both full-length and ZP domain sequences supported a phylogenetic root between the ZPC subfamily and the remainder of the tree.
These findings provide some evidence that the first event in ZP evolution was a gene duplication event, which gave rise to the ancestral ZPC gene and to the precursor of the ZPA, ZPB, and ZPX subfamilies. This precursor duplicated at least three times over a short period of evolutionary history, giving rise to the ancestral ZPX genes and the ancestral ZPA and ZPB genes. These events all occurred early during vertebrate evolution, before evolution of the first amphibians. Subsequently, duplication events have occurred in several lineages, with the most notable occurring early during evolution of the amniotes and giving rise to the ZPB1 and ZPB2 groups within the ZPB subfamily.
Other important observations and conclusions can be inferred from the tree shown in Figure 1. First, a consistent grouping, supported by all the phylogenetic methods used, of the Gallus gallus (chicken) and Trichosurus vulpecula (brush-tailed possum) ZPC genes to the exclusion of other ZPC genes is observed. A possible explanation for this relationship is that the chicken and possum ZPC genes are paralogous to the eutherian ZPC genes. Second, the gene duplication that gave rise to the ZPA genes occurred before the divergence of fish and amphibians; therefore, at some point during evolution, fish had a ZPA gene. Fish have either lost the ZPA gene or have an as-yet-unidentified ZPA gene or pseudogene. The alternate possibilities, that the fish ZP genes evolved from a ZPA/ZPB precursor or that the ZPX1 genes are actually ZPA orthologues, are phylogenetically unlikely. Third, the ZPX genes originated from duplications before the divergence of fish and amphibians. It is anticipated that genes currently present in fish and amphibians were also present in early amniotes. The absence of any known ZPX orthologues in extant amniotes suggests the loss of ZPX precursors early during amniote evolution.
| ZP GENE NOMENCLATURE |
|---|
|
|
|---|
and ß become ZPBa and ZPBb, respectively). In all cases, the gene name should follow the hierarchy of the phylogeny: subfamily first (uppercase letter), then group (number, when appropriate), and finally, a paralogue label (lowercase letter, when appropriate). We have made an exception in the nomenclature system for the two X. laevis genes and the O. latipes gene that have no known amniote orthologues. To ensure that the X. laevis and O. latipes ZPA, ZPB, and ZPC genes have the same name as their orthologues, these three sequences are named ZPX1 and ZPX2 (Table 1).
This is only an initial attempt to create a logical system of nomenclature. It is designed to air the current problems and to promote discussion of possible solutions. We propose that those individuals with interest in the ZP genes and proteins establish a working group to examine the problems surrounding the present systems of nomenclature and make recommendations for a new system that would find wide acceptance.
| ACKNOWLEDGMENTS |
|---|
| FOOTNOTES |
|---|
Received: 10 June 2002.
First decision: 25 June 2002.
Accepted: 8 July 2002.
| REFERENCES |
|---|
|
|
|---|
This article has been cited by other articles:
![]() |
E. Menkhorst and L. Selwood Vertebrate Extracellular Preovulatory and Postovulatory Egg Coats Biol Reprod, November 1, 2008; 79(5): 790 - 797. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. M. Wassarman Zona Pellucida Glycoproteins J. Biol. Chem., September 5, 2008; 283(36): 24285 - 24289. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. Goudet, S. Mugnier, I. Callebaut, and P. Monget Phylogenetic Analysis and Identification of Pseudogenes Reveal a Progressive Loss of Zona Pellucida Genes During Evolution of Vertebrates Biol Reprod, May 1, 2008; 78(5): 796 - 806. [Abstract] [Full Text] [PDF] |
||||
![]() |
T. Sasanami, T. Murata, M. Ohtsuki, K. Matsushima, G. Hiyama, N. Kansaku, and M. Mori Induction of sperm acrosome reaction by perivitelline membrane glycoprotein ZP1 in Japanese quail (Coturnix japonica) Reproduction, January 1, 2007; 133(1): 41 - 49. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. Okumura, N. Aoki, C. Sato, D. Nadano, and T. Matsuda Heterocomplex Formation and Cell-Surface Accumulation of Hen's Serum Zona Pellucida B1 (ZPB1)with ZPC Expressed by a Mammalian Cell Line (COS-7): A Possible Initiating Step of Egg-Envelope Matrix Construction Biol Reprod, January 1, 2007; 76(1): 9 - 18. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. E. Aagaard, X. Yi, M. J. MacCoss, and W. J. Swanson Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs PNAS, November 14, 2006; 103(46): 17302 - 17307. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Modig, T. Modesto, A. Canario, J. Cerda, J. v. Hofsten, and P.-E. Olsson Molecular Characterization and Expression Pattern of Zona Pellucida Proteins in Gilthead Seabream (Sparus aurata) Biol Reprod, November 1, 2006; 75(5): 717 - 725. [Abstract] [Full Text] [PDF] |
||||
![]() |
X. Liu, H. Wang, and Z. Gong Tandem-Repeated Zebrafish zp3 Genes Possess Oocyte-Specific Promoters and Are Insensitive to Estrogen Induction Biol Reprod, June 1, 2006; 74(6): 1016 - 1025. [Abstract] [Full Text] [PDF] |
||||
![]() |
S.M. Mackenzie, E.A. McLaughlin, H.D. Perkins, N. French, T. Sutherland, R.J. Jackson, B. Inglis, W.J. Muller, B.H. van Leeuwen, A.J. Robinson, et al. Immunocontraceptive Effects on Female Rabbits Infected with Recombinant Myxoma Virus Expressing Rabbit ZP2 or ZP3 Biol Reprod, March 1, 2006; 74(3): 511 - 521. [Abstract] [Full Text] [PDF] |
||||
![]() |
Y. Shen, T. Stalf, C. Mehnert, U. Eichenlaub-Ritter, and H.-R. Tinneberg High magnitude of light retardation by the zona pellucida is associated with conception cycles Hum. Reprod., June 1, 2005; 20(6): 1596 - 1606. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. von Witzendorff, M. Ekhlasi-Hundrieser, Z. Dostalova, M. Resch, D. Rath, H.-W. Michelmann, and E. Topfer-Petersen Analysis of N-linked glycans of porcine zona pellucida glycoprotein ZPA by MALDI-TOF MS: a contribution to understanding zona pellucida structure Glycobiology, May 1, 2005; 15(5): 475 - 488. [Abstract] [Full Text] [PDF] |
||||
![]() |
S.J. Conner, L. Lefievre, D.C. Hughes, and C.L.R. Barratt Cracking the egg: increased complexity in the zona pellucida Hum. Reprod., May 1, 2005; 20(5): 1148 - 1152. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. G. Blackmore, L. R. Baillie, J. E. Holt, L. Dierkx, R. J. Aitken, and E. A. McLaughlin Biosynthesis of the Canine Zona Pellucida Requires the Integrated Participation of Both Oocytes and Granulosa Cells Biol Reprod, August 1, 2004; 71(2): 661 - 668. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. Bogner, K.-D. Hinsch, P. Nayudu, L. Konrad, C. Cassara, and E. Hinsch Localization and synthesis of zona pellucida proteins in the marmoset monkey (Callithrix jacchus) ovary Mol. Hum. Reprod., July 1, 2004; 10(7): 481 - 488. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. Lefievre, S.J. Conner, A. Salpekar, O. Olufowobi, P. Ashton, B. Pavlovic, W. Lenton, M. Afnan, I.A. Brewis, M. Monk, et al. Four zona pellucida glycoproteins are expressed in the human Hum. Reprod., July 1, 2004; 19(7): 1580 - 1586. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Rodeheffer and B. D. Shur Characterization of a novel ZP3-independent sperm-binding ligand that facilitates sperm adhesion to the egg coat Development, February 1, 2004; 131(3): 503 - 512. [Abstract] [Full Text] [PDF] |
||||
![]() |
T. Sasanami, A. M. Hanafy, M. Toriyama, and M. Mori Variant of Perivitelline Membrane Glycoprotein ZPC of Japanese Quail (Coturnix japonica) Lacking Its Cytoplasmic Tail Exhibits the Retention in the Endoplasmic Reticulum of Chinese Hamster Ovary (CHO-K1) Cells Biol Reprod, October 1, 2003; 69(4): 1401 - 1407. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. S. Boja, T. Hoodbhoy, H. M. Fales, and J. Dean Structural Characterization of Native Mouse Zona Pellucida Proteins Using Mass Spectrometry J. Biol. Chem., September 5, 2003; 278(36): 34189 - 34202. [Abstract] [Full Text] [PDF] |
||||
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |