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Proc Natl Acad Sci U S A. Apr 25, 2006; 103(17): 6560–6564.
Published online Apr 12, 2006. doi:  10.1073/pnas.0510440103
PMCID: PMC1564201
Developmental Biology

A pair-rule gene circuit defines segments sequentially in the short-germ insect Tribolium castaneum


In Drosophila, a hierarchy of maternal, gap, pair-rule, and segment polarity gene interactions regulates virtually simultaneous blastoderm segmentation. For the last decade, studies have focused on revealing the extent to which Drosophila segmentation mechanisms are conserved in other arthropods where segments are added sequentially from anterior to posterior in a cellular environment. Despite our increased knowledge of individual segmentation genes, details of their interactions in non-Drosophilid insects are not well understood. We analyzed the Tribolium orthologs of Drosophila pair-rule genes, which display pair-rule expression patterns. Tribolium castaneum paired (Tc-prd) and sloppy-paired (Tc-slp) genes produced pair-rule phenotypes when their transcripts were severely reduced by RNA interference. In contrast, similar analysis of T. castaneum even-skipped (Tc-eve), runt (Tc-run), or odd-skipped (Tc-odd) genes produced severely truncated, almost completely asegmental phenotypes. Analysis of interactions between pair-rule components revealed that Tc-eve, Tc-run, and Tc-odd form a three-gene circuit to regulate one another as well as their downstream targets, Tc-prd and Tc-slp. The complement of primary pair-rule genes in Tribolium differs from Drosophila in that it includes Tc-odd but not Tc-hairy. This gene circuit defines segments sequentially in double segment periodicity. Furthermore, this single mechanism functions in the early blastoderm stage and subsequently during germ-band elongation. The periodicity of the Tribolium pair-rule gene interactions reveals components of the genetic hierarchy that are regulated in a repetitive circuit or clock-like mechanism. This pair-rule gene circuit provides insight into short-germ segmentation in Tribolium that may be more generally applicable to segmentation in other arthropods.

Keywords: insect segmentation, even-skipped, runt, odd-skipped

In Drosophila, a hierarchy of maternal, gap, pair-rule, and segment polarity genes regulates segmentation (1). Pair-rule genes transform regional gradients of maternal and gap gene information into cellular domains that define parasegmental boundaries (2), ultimately producing segments by means of regulation of segment polarity genes. Genetic and molecular analyses reveal a complex pair-rule gene network, which operates in units of double segment periodicity. even-skipped (eve), hairy (h), and runt (run) are essential in setting parasegmental boundaries. These primary pair-rule genes are regulated by the maternal and gap genes; in turn, they regulate other, secondary pair-rule genes such as fushi-tarazu (ftz), paired (prd), sloppy-paired (slp), and odd-skipped (odd) (3, 4). In general, loss of primary pair-rule gene function affects the expression of secondary pair-rule genes, whereas the expression of primary pair-rule genes is not altered in secondary pair-rule gene mutants.

Comparative studies of pair-rule gene homologs in other insects reveal a wide variety of expression patterns. In the grasshopper Schistocerca, homologs of eve and ftz are not expressed in pair-rule stripes (5, 6). In the milkweed bug Oncopeltus fasciatus, the eve homolog is expressed in segmental, not pair-rule, stripes (7). In the beetle Tribolium castaneum, where eve, ftz, h, and run orthologs are expressed in pair-rule stripes (810), loss of ftz does not produce a pair-rule phenotype (11). However, pair-rule expression of prd homologs is conserved in Drosophila, Tribolium, and Schistocerca (12). These results suggest that if insect segments are prepatterned in units of double segment periodicity, then the genetic regulatory interactions of pair-rule mechanisms differ in each species.

Interactions among pair-rule genes in insects other than Drosophila have not been investigated to date. We have used parental RNA interference (RNAi) (13) to functionally analyze pair-rule gene orthologs and their interactions in the short-germ beetle T. castaneum. Here, we describe the genetic interactions of pair-rule patterning in the short-germ insect T. castaneum and discuss implications for insect segmentation.


Two Classes of Pair-Rule Genes in Tribolium.

Classic pair-rule mutant phenotypes in Drosophila include loss of alternating segments or defects displaying double segment periodicity, which are consistent with the normal expression pattern of the corresponding gene. Because Tribolium orthologs of these genes are expressed in pair-rule patterns (see Fig. 5 and Supporting Results, which are published as supporting information on the PNAS web site, for expression of Tc-odd, Tc-prd, and Tc-slp), we expected RNAi to produce similar phenotypes. Surprisingly, however, strong knock-down of Tc-eve, Tc-run, or Tc-odd transcripts produced truncated, almost completely asegmental embryos instead of pair-rule phenotypes. Tc-eveRNAi embryonic cuticles contain labrum, antennae, and telson (Fig. 1b) but no gnathal or trunk segments. In addition to labrum and antennae, Tc-runRNAi cuticles contain mandibles (Fig. 1c), whereas Tc-oddRNAi cuticles contain mandibles and maxilla (Fig. 1d). Consistent with these phenotypes, there are no gnathal or trunk Tc-Engrailed (Tc-En) stripes in Tc-eveRNAi germ-band embryos, and only one (mandibular) or two gnathal (mandibular and maxillary) stripes in Tc-run and Tc-odd RNAi embryos (Fig. 2g, m, and s), respectively. The homeotic gene Tc-Dfd, which serves as a molecular marker for mandibular and maxillary segments, is expressed normally in Tc-oddRNAi embryos (Fig. 2s). Knock-down of any of these three genes blocked segmentation and elongation. In Drosophila, eve null mutants produce asegmental cuticles, whereas null mutants of run or odd cause typical pair-rule phenotypes (14). The similar truncated, asegmental phenotypes of Tc-eve RNAi, Tc-runRNAi, and Tc-oddRNAi embryos suggest that these genes function at the same level in the segmentation hierarchy.

Fig. 1.
Cuticle preparations of severely affected T. castaneum pair-rule gene RNAi embryos. (a) This WT first-instar larval cuticle contains a head, three thoracic segments (T1–T3), eight abdominal segments (A1–A8), and terminal structures. Lr, ...
Fig. 2.
Expression of Tribolium pair-rule genes in primary pair-rule gene RNAi embryos. Expression of Tc-En and pair-rule genes in WT (af), Tc-eveRNAi (gl), Tc-runRNAi (mr), and Tc-oddRNAi (s-x) embryos is shown. (g) Antennal and intercalary ...

In contrast, Tc-prdRNAi and Tc-slpRNAi generated typical pair-rule phenotypes (Fig. 1 e and f) that phenocopy previously described mutants (15). Similar to Drosophila prd mutants (14), Tc-prdRNAi embryonic cuticles lacked odd-numbered segments, including mandibular, labial, thoracic (T2), and four abdominal segments (Fig. 1e). Corresponding germ-band embryos lacked odd-numbered Tc-En stripes (Fig. 3c and d), suggesting that Tc-prd is essential for the expression of Tc-En in odd-numbered parasegments. Complementary to Tc-prdRNAi, Tc-slpRNAi cuticles lacked even-numbered segments (Fig. 1f). Corresponding germ-band embryos lacked even-numbered Tc-En stripes (Fig. 3 e and f), indicating that Tc-slp is required for the expression of Tc-En in even-numbered parasegments. Interestingly, hypomorphic slp mutants in Drosophila affect odd-numbered segments (16), whereas Tc-slpRNAi affects even-numbered segments, implying that the requirement for slp function is different in flies and beetles.

Fig. 3.
Tc-En staining reveals pair-rule defects in severely affected secondary T. castaneum pair-rule gene RNAi embryos. (a) Sixteen Tc-En stripes are visible in this fully elongated WT germ band. (b) Tc-run is transiently expressed in even-numbered parasegments ...

The two classes of cuticular phenotypes seen in RNAi embryos suggest that in Tribolium, pair-rule genes may operate at two functional levels, as in Drosophila. In addition, nascent stripes of Tc-run and Tc-odd appear in the posterior growth zone, whereas stripes of Tc-prd and Tc-slp appear later in the anterior growth zone (see Fig. 4a and Supporting Results). Taken together, these data suggest that Tc-eve, Tc-run, and Tc-odd may function as primary pair-rule genes, whereas Tc-prd and Tc-slp function as secondary pair-rule genes.

Fig. 4.
Pair-rule patterning in Tribolium. (a) The dynamic expression of the primary and secondary pair-rule genes and their regulatory interactions are summarized. The bar at the top indicates that anterior is to the left. Newer segments forming in the growth ...

We also analyzed the functions of the remaining candidate pair-rule genes, Tribolium h, ftz, odd-paired (opa), and Tenascin major (Ten-m). However, no segmentation defects were observed (data not shown), with the exception of Tc-hRNAi, which produced anterior defects (Fig. 6 and Supporting Results, which are published as supporting information on the PNAS web site). The truncated, asegmental phenotypes shown by Tc-eveRNAi, Tc-runRNAi, and Tc-oddRNAi embryos; the modified pair-rule function of Tc-slp; and the fact that not all pair-rule gene orthologs participate in segmentation in Tribolium strongly suggest that segments are prepatterned by different pair-rule gene interactions in Tribolium and Drosophila.

Epistasis Analysis of Tc-eve, Tc-run, and Tc-odd.

To understand how genes expressed in pair-rule stripes produce truncated and asegmental RNAi embryonic cuticles, we examined the RNAi effects of each gene on the expression of the others. In severely affected Tc-eveRNAi embryos, expression of Tc-run and Tc-odd was lost or greatly reduced, indicating that Tc-eve is required for the activation of Tc-run and Tc-odd (Fig. 2 hj). The expression patterns of Tc-eve and Tc-odd are almost completely complementary and show only slight overlap (Fig. 5b). Therefore, Tc-eve probably indirectly activates Tc-odd. In severely affected Tc-oddRNAi embryos, the broad initial expression domains of Tc-eve and Tc-run failed to resolve into pair-rule stripes (Fig. 2 tv). Thus, Tc-odd is required for repression of Tc-eve and Tc-run to produce pair-rule stripes. However, it is unlikely that Tc-odd directly represses Tc-run, because their expression patterns overlap (Fig. 4a and Supporting Results). Instead, Tc-odd might repress Tc-run through repression of Tc-eve. In Drosophila, the initial expression of the primary pair-rule genes eve and run is not altered by mutations in odd (17), a secondary pair-rule gene. The ectopic expression of Tc-eve and Tc-run in Tc-oddRNAi indicates that different genetic interactions between these genes evolved in the lineages, leading to beetles and flies. Strongly affected Tc-runRNAi caused broad expression of Tc-eve as well as severe reduction of Tc-odd expression in the growth zone, implying that Tc-run is required for activation of Tc-odd and repression of Tc-eve (Fig. 2 np). However, the overlap between Tc-eve and Tc-run expression (Fig. 7, which is published as supporting information on the PNAS web site) suggests that the repression of Tc-eve by Tc-run is an indirect effect mediated by Tc-odd. These interactions indicate that these three genes provide primary pair-rule functions in Tribolium.

Tc-prd and Tc-slp Are Secondary Pair-Rule Genes.

To understand whether Tc-prd and Tc-slp function as primary or secondary pair-rule genes, we analyzed the effect of Tc-prd or Tc-slp RNAi on the expression of the others. The expression of Tc-eve, Tc-run, or Tc-odd was not altered in Tc-prdRNAi or Tc-slpRNAi embryos (data not shown). However, the stripes of Tc-prd and Tc-slp failed to resolve in Tc-eveRNAi and Tc-runRNAi embryos (Fig. 2 k, l, q, and r), probably because of the absence of interstripe repression. In contrast, Tc-prd and Tc-slp expression was abolished in the growth zone of Tc-oddRNAi embryos (Fig. 2 w and x), suggesting that Tc-prd and Tc-slp provide pair-rule functions that are secondary to those of Tc-eve, Tc-run, and Tc-odd. In addition, Tc-prd was expressed normally in Tc-slpRNAi embryos, and Tc-slp was expressed normally in Tc-prdRNAi embryos (data not shown), indicating that they do not interact with each other and are in parallel positions in the pathway. Although Tc-prd and Tc-slp were misregulated by the knock-down of the three primary pair-rule genes, it seems likely that Tc-eve and Tc-odd regulate Tc-prd and Tc-slp indirectly through Tc-run; Tc-prd and Tc-slp were misregulated by knockdown of each of the three primary pair rule genes. However, only the expression of Tc-run was consistently correlated with the misregulation of Tc-prd and Tc-slp in the three RNAi backgrounds (compare Fig. 2 i, o, and u with Fig. 2 l, r, and x, respectively). These results place them downstream of Tc-run.

Tribolium Pair-Rule Genes Do Not Act Upstream of Gap Genes.

Depletion of eve mRNA in the milkweed bug Oncopeltus fasciatus results in misregulation of gap genes, producing a severely affected head-only phenotype (7). To determine whether misregulation of gap genes contributed to the asegmental phenotypes observed in Tc-eveRNAi, Tc-runRNAi, and Tc-oddRNAi embryos, we examined their expression in RNAi germ-band embryos. Expression of the Tribolium orthologs of hunchback, Krüppel, giant, and knirps are largely normal in the RNAi embryos (data not shown), suggesting that the asegmental phenotypes generated by RNAi for Tribolium pair-rule genes are not due to the misregulation of Tribolium gap genes.


We analyzed the functions and interactions of the Tribolium homologs of Drosophila pair-rule genes by using RNAi. We discovered that the Tribolium homologs of eve, run, and odd function as primary pair-rule genes and that prd and slp function as secondary pair-rule genes but that h, ftz, opa, and Ten-m do not function as pair-rule genes. Severe knock-down of Tribolium primary pair-rule genes led to truncated, asegmental phenotypes, whereas depletion of secondary pair-rule genes produced classic pair-rule phenotypes. Based on these discoveries, we propose a model of pair-rule patterning in Tribolium that might explain the RNAi phenotypes and discuss major differences in the interactions of pair-rule genes in Drosophila and Tribolium. Finally, we discuss the implications of these findings on segmentation in short-germ insects and other arthropods.

A Model of Pair-Rule Gene Interaction in Tribolium.

We describe a pair-rule gene circuit in Fig. 4a in which Tc-eve expression is required to activate Tc-run, which, in turn, is required to activate Tc-odd. Tc-odd expression in even-numbered parasegments is required to repress Tc-eve there, separating a primary Tc-eve stripe from the broad expression domain. As Tc-eve expression is repressed in even-numbered parasegments, the posterior edges of Tc-run and then Tc-odd expression fade. Tc-eve expression is also repressed in odd-numbered parasegments (regulated by an as yet unknown gene) to produce segmental Tc-eve secondary stripes that are coincident with Tc-En stripes (8, 18). Loss of Tc-eve expression in odd-numbered parasegments causes Tc-run stripes to fade from their anterior edge, resulting in narrow Tc-run stripes that are coincident with every even-numbered Tc-En stripe. For reasons yet unknown, all three genes remain coexpressed with Tc-En in even-numbered parasegments. Consequently, a two-segment unit is prepatterned through one cycle of this primary pair-rule gene circuit. Restriction of Tc-run expression leads to the derepression of Tc-prd and Tc-slp, which are responsible for the activation of Tc-En in odd- and even-numbered parasegments, respectively.

The asegmental phenotypes produced by RNAi analysis of Tc-eve, Tc-run, and Tc-odd are readily explained by this model. The knock-down of Tc-eve abolishes Tc-run expression, which induces ectopic expression of both Tc-prd and Tc-slp. Tc-En expression is not properly regulated to define the parasegmental borders, which results in an asegmental phenotype. Similarly for Tc-runRNAi, in the absence of Tc-run, Tc-prd and Tc-slp are expressed ectopically, Tc-En is not activated, and segmental grooves are not formed. However, the mechanism that generates the asegmental phenotype in Tc-oddRNAi embryos is different from that in Tc-eveRNAi or Tc-runRNAi embryos; the knock-down of Tc-odd leads to ectopic expression of Tc-eve, which induces ectopic expression of Tc-run. As a result, Tc-prd and Tc-slp are fully repressed, which leads to misregulation of Tc-En expression and produces the asegmental Tc-oddRNAi phenotype. Thus, either loss or ectopic expression of Tc-prd or Tc-slp leads to misregulation of Tc-En, ultimately resulting in asegmental phenotypes.

Major Differences of Pair-Rule Interactions Between Drosophila and Tribolium.

Our model of pair-rule interactions in Tribolium is not predicted by simple application of the Drosophila pair-rule gene paradigm (19) (Fig. 4b). In Drosophila, the three primary pair-rule genes (h, eve, and run) are key players in initiating pair-rule patterning. However, Tc-h seems not to function as a pair-rule gene at all. Although odd is a secondary pair-rule gene in Drosophila that is repressed by eve, Tc-odd functions as a primary pair-rule gene in Tribolium that represses Tc-eve. Repression of slp and odd by eve is critical to activate prd-dependent odd-numbered and ftz-dependent even-numbered en stripes, respectively, in Drosophila (19, 20) (Fig. 4b). In contrast, Tc-eve is required for the activation of Tc-odd, which in turn represses Tc-eve to prepattern a two-segment unit. Furthermore, Tc-run, which is induced by Tc-eve, is important for the formation of Tc-prd-dependent odd-numbered and Tc-slp-dependent even-numbered Tc-en stripes. Drosophila ftz is a secondary pair-rule gene that activates even-numbered en stripes, but Tc-ftz does not function in segmentation (11). Differences in the primary pair-rule genes result in different genetic interactions between primary and secondary genes and likely affect the regulatory interactions between pair-rule and segment polarity genes. For example, loss of slp affects odd- numbered parasegments, whereas loss of Tc-slp affects even-numbered parasegments.

Our model provides a core mechanism for pair-rule patterning in Tribolium segmentation. However, additional components remain to be discovered. Tc-eve, Tc-run, and Tc-odd have different anterior boundaries of expression that correspond to the number of gnathal segments remaining in RNAi embryos. These boundaries are likely regulated by gap genes, as in Drosophila.

By using the candidate gene approach, we determined that orthologs of genes previously identified as pair-rule genes in Drosophila function in Tribolium segmentation. However, the gene(s) responsible for resolution of primary pair-rule Tc-eve stripes into secondary segmental stripes as well as genes that limit the expression of Tc-run within the Tc-eve domain and Tc-odd within the Tc-run domain have yet to be determined. Furthermore, we do not yet know which genes function to activate Tc-prd and Tc-slp. It still must be determined how the pair-rule gene circuit is initiated in blastoderm embryos and stopped after elongation. If this pair-rule gene circuit is regulated by genes involved in anterior–posterior patterning, Tc-caudal is a likely candidate. It is strongly expressed in the growth zone throughout germ-band elongation (21, 22) and produces a severely affected RNAi phenotype (23) that is identical to that described for Tc-eve. Gap genes such as Tc-hunchback, which is expressed in the posteriormost regions of the elongating germ band (24), may be involved in regulating the pair-rule gene circuit there. However, because pair-rule patterning occurs in a cellular environment in Tribolium, it is possible that intercellular signaling pathways are involved in regulating the pair-rule gene circuit as components or targets of a segmentation clock. Indeed, the sequential function of the pair-rule gene circuit during Tribolium segmentation provides evidence for regulation by some type of periodic mechanism in insects. In vertebrates, somitogenesis is regulated by a segmentation clock (25). Homologs of vertebrate segmentation clock components, such as Notch and Delta, are required for proper segmentation in basally branching arthropods such as the spider Cupiennius and have led to the speculation that this mode of segmentation might be very ancient (26). Although a Notch homolog has not been implicated in insect segmentation (27), other signaling molecules may provide the regulatory link between pair-rule genes and a segmentation clock.

Primary Pair-Rule Genes in Germ-Band Elongation.

In Tribolium, a short, wide germ rudiment elongates into a long, narrow germ band during segmentation (28). In the absence of concerted cell division, this morphological change may be due to cell movement and intercalation, similar to convergent extension in Drosophila (29). Germ-band elongation is not disrupted in Tc-prd and Tc-slp RNAi embryos; the classic pair-rule phenotypes result from loss of patterning in alternating segments. In contrast, defective elongation in Tc-eve, Tc-run, and Tc-odd RNAi embryos produces short, amorphous germ bands in which posterior segments are not initiated. These results, taken together with their WT expression patterns, implicate primary (but not secondary) pair-rule genes in elongation as well as segmentation. Interestingly, eve and run have been implicated in convergent extension of the Drosophila germ band (29).

One Segmentation Mechanism Functions in the Blastoderm and During Elongation.

In Tribolium, up to three pair-rule stripes form in the cellular blastoderm, prepatterning the three gnathal and three thorax segments; abdominal segments are subsequently added from the growth zone during germ-band elongation. Gap gene RNAi and mutant phenotypes display specific homeotic phenotypes in the gnathum and thorax with severely disrupted segmentation in the abdomen (30, 31). These results have led to the hypothesis that segmentation mechanisms differ between the blastoderm and elongation phases of short-germ development. The pair-rule gene circuit that we describe prepatterns segments in double segment periodicity from the gnathum through the abdomen, providing continuity between the blastoderm and germ-band elongation phases. Thus, it appears that the biggest difference between these phases occurs at the level of the gap genes.

Several Insights into Segmentation in Other Short-Germ Arthropods.

Our results provide several insights into segmentation in Tribolium that may apply to other short-germ arthropods in general. First, a smaller complement of genes may comprise the core pair-rule mechanism. Second, primary and secondary genes may be different from those in Drosophila. Indeed, the dynamics of pair-rule gene homolog expression in the spider Cupiennius (32) suggest pair-rule gene functions that differ from those of their Drosophila counterparts. Third, if primary pair-rule genes function in both elongation and segmentation in short-germ arthropods, they may produce dramatically stronger RNAi phenotypes than secondary pair-rule genes. RNAi analysis in more nonmodel arthropods is required to test these insights and provide a better understanding of the logic of the ancestral pair-rule patterning mechanism.

Materials and Methods

Molecular Analysis.

Tc-odd, Tc-prd, and Tc-slp sequences were computationally identified in the Tribolium genome sequence by tblastn analysis of Drosophila protein sequences. PCR amplicons from total embryonic RNA were cloned to use as templates for in situ probes or dsRNA.

Parental RNAi.

Parental RNAi was performed as described in ref. 13. Injection of 900 ng/μl (Tc-eve), 500 ng/μl (Tc-run, Tc-prd, and Tc-slp), or 350 ng/μl (Tc-odd) into pupae produced strong RNAi effects. Injection buffer (1×) or 1 μg/μl Tc-ftz dsRNA was injected and produced no mutant effects.

Whole-Mount in Situ Hybridization and Immunocytochemistry.

Whole-mount in situ hybridization was carried out as in refs. 8 and 9 with digoxigenin-labeled RNA probes. The anti-digoxigenin antibody conjugated with alkaline phosphatase (Roche Diagnostics) was preadsorbed and used at a 1/2,000 dilution. Immunocytochemistry was performed as described in ref. 8 with the anti-Eve antibody diluted to 1/20 or the anti-En antibody diluted to 1/5. Germ bands were dissected from the yolks of embryos, mounted in 80% glycerol, and photographed using Nomarski optics on a BX50 compound microscope (Olympus, Melville, NY).

Phenotype Analysis.

Cuticle preparations of RNAi embryos were performed as described in ref. 11. First-instar larvae were observed and photographed under dark-field optics.

Supplementary Material

Supporting Information:


We thank T. Shippy, Y. Tomoyasu, R. Denell, and M. Klingler for valuable discussions and critical reading of the manuscript and the Baylor Human Genome Sequencing Center (Houston) for Tribolium genomic sequences. This work was supported by a grant from the National Institutes of Health (to S.J.B.).


RNA interference


Conflict of interest statement: No conflicts declared.

This paper was submitted directly (Track II) to the PNAS office.

Data deposition: The sequences reported in this paper have been deposited in the GenBank database [accession nos. DQ414246 (Tc-odd), DQ414247 (Tc-prd), and DQ414248 (Tc-slp)].


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