# Patent

## Title
C. elegans p21-activated kinase (PAK) gene and associated loss-of-function phenotypes that facilitate screening for small molecule modulators of PAK activity in the nematode, caenorhabditis elegans

## Abstract

The invention refers to a novel C. elegans p21-activated kinase gene, the pak-3 gene, and associated loss-of-function phenotypes. These phenotypes can be used to elucidate PAK signaling pathways in C. elegans and to screen compounds that modulate PAK signaling.

## Background
A novel C. elegans p21-activated kinase (PAK) gene and associated loss-of-function phenotypes that facilitate screening for small molecule modulators of PAK activity in the nematode, Caenorhabditis elegans. 
The invention refers to a novel C. elegans p21-activated kinase gene, the pak-3 gene, and associated loss-of-function phenotypes. These phenotypes can be used to elucidate PAK signaling pathways in C. elegans and to screen compounds that modulate PAK signaling.
The p21-activate kinases comprise a group of serine/threonine protein kinases with distinct structural features that have emerged as important regulators of several different cellular and biological processes (reviewed in Bokoch, Annu Rev Biochem 2003. 72:743-81). The PAK family can be subdivided in the PAK 1-3 subclass and the PAK 4-6 subclass (based on the numbering of the human/mammalian PAKs), the former being the focus of interest here. Members of the PAK 1-3 subclass are highly related to the STE20 kinase in yeast, the founding member of this protein class, and homologous have also been identified in other model organisms such as Drosophila and C. elegans. 
The two most important structural features of PAKs of the 1-3 class are the highly conserved C-terminal catalytic domain and the N-terminal regulatory domain, respectively. A distinct motif in the regulatory domain of PAK proteins in the CRIB domain (cdc42 and Rac interactive domain), which overlaps with an autoinhibitory domain, keeping the catalytic domain inactive in the absence of stimulatory signals. Other motifs found in PAK proteins are SH3 binding domains and an acidic residue-rich domain between the regulatory domain and the catalytic domain. Additionally a binding site for the Gβγ subunit of heterotrimeric G proteins has been reported to be present in the very C-terminus of PAK.
The most well described activators of PAKs are the Rho class GTPases cdc42 and Rac that upon binding to the CRIB domain block the autoinhibitory domain, leading to activation of the kinase domain. Activation of PAKs can also take place through GTPase independent mechanisms after recruitment of PAKs to the plasma membrane where tyrosine kinase receptor mediated activation occurs. PAKs are known to be activated by phosphorylation, in part through autophosphorylation at Thr423 and Ser144 (numbering according to human PAK1). One kinase that has been shown to phosphorylate Thr423 is PDK1, a 3-phosphinositide dependent kinase.
Many proteins have been reported to be phosphorylated by PAKs, several of those are proteins involved in cell structure and cell motility. It has for example been shown that LIM kinases-1 and -2, serine kinases implicated in actin cytoskeletal dynamics, are phosphorylated by PAKs. Other targets involved in cell motility are myosin light chain kinase and regulatory myosin light chain. In addition PAKs are involved in microtubule dynamics, possibly by phosphorylation of stathmin.
Through their regulatory actions on the actin cytoskeleton, myosin, and microtubules, PAKs are highly involved in cellular processes such as cell motility and cell migration, which on the organism level is manifested as important role(s) for PAKs during e.g. neurogenesis and angiogenesis. It has also been suggested that PAKs are part of a signaling cascade leading to platelet activation through their regulatory action on actin cytoskeleton dynamics. PAKs are known to have both pro- and antiapoptotic effects, depending on the isoform in question. PAK2 is activated by caspase 3 and is thus part of the apoptotic signaling cascade, whereas it has been reported that PAK1 is activated by certain signaling pathways that promote cell survival, for example by IL-3 signaling.
The important role for PAKs in neurogenesis is exemplified by the hereditary disease nonsyndromic X-linked mental retardation, which is caused by point mutations in PAK3, the brain-specific PAK isoform in humans.
Several studies have suggested that PAKs may play important roles in cancer metastasis. So has it been reported that many breast cancer cell lines express elevated PAK1 and PAK2 activities. It has also been shown that heregulin, a stimulator of cancer cell growth stimulates PAK1 activity. In additional, dominant negative forms of Pak1 can inhibit motility and invasiveness in cancer cell model.
Is has been demonstrated that PAKs can associate with the HIV encoded Nef protein, a protein of central importance in HIV pathogenesis. Together with Nef, PAK appears to promote viral replication an pathogenesis of HIV, and PAK is required for survival of infected cells.
Previous studies have described the existence of one PAK encoding gene in C. elegans, denoted PAK1 (Chen et al 1996 JBC 271, 26362-68, lino & Yamamoto 1998 BBRC 245, 177-84). It was shown by in vitro biochemical assays that PAK1 encodes a bona fide PAK protein demonstrating kinase activity and interaction with CeRac1 (today known as CED-10) and CDC42Ce (CDC-42). Immunoflourescence indicated PAK-1 localization to hypodermal cell boundaries during embryonic body elongation, suggesting a role for pak-1 in embryogenesis. Analysis of transgenic worms expressing pak-1 promoter-reporter gene fusions demonstrated pak-1 expression throughout development, primarily in embryonic tissues, pharyngeal muscles, CAN neurons, motor neurons in the ventral nerve cord, the spermatheca and the distal tip cell (DTC) of the developing gonad. However, no in vivo functional characterization of pak-1 has been reported, even though a knock-out pak-1 strain, RB689, is publicly available. This might suggest that loss-of-function phenotypes of pak-1 are very subtle and hard to detect or that pak-1 is functionally redundant with other protein(s).
C45b11.1 (pak-4)
In addition to the pak-1 gene, one other predicted gene in the C. elegans genome, c45b11.1, appears to encode a PAK protein, which, based on sequence homology, belongs to the PAK 4-6 subclass of PAK proteins. We propose to call this gene pak-4.
Indications of a hitherto unidentified pak gene
Sequence homology searches for genes encoding PAK-like kinase domains identified one open reading frame, y38f1a.10 (SEQ. ID NO. 33), predicted to encode a kinase domain-only protein, without the characteristic regulatory regions of a PAK protein. In the kinase database “kinase.com” located on the world wide web, this ORF is denoted with the name PAK3 with the associated comment that a putative CRIB domain is encoded in a genomic region further upstream. However, no references or experimental data is provided that support this notion.
The invention pertains to an isolated polynucleotide comprising a DNA sequence which is selected from one of the following groups

    
    
        a] a DNA sequence of SEQ ID NO. 1; or
        b] a DNA sequence which is complementary to SEQ ID NO. 1; or
        c] a DNA sequence which hybridizes to a DNA sequence of SEQ ID NO. 1 or to a DNA sequence which is complementary to SEQ ID NO. 1; or
        d] a DNA sequence which is degenerate as a result of the genetic code to the DNA sequence of SEQ ID NO. 1 or to a DNA sequence which is complementary to SEQ ID NO. 1; or
        e] a DNA sequence which is encoding a pak-3a polypeptide.
    
    


In one embodiment of the invention the isolated polynucleotide consists of a polynucleotide sequence of SEQ ID NO. 1.
In a further embodiment of the invention the pak-3a polypeptide that is encoded by the DNA-sequence is the pak-3a polypeptide of C. elegans consisting of an amino acid sequence of SEQ ID NO. 7.
The hybridization can occur under conditions of medium or high stringency. Conditions of medium or high stringent hybridization can be found in textbooks as

    
    
        “Molecular Cloning; edited by Sambrook J. Fritsch E. F. , Maniatis T.; Cold Spring Harbor Laboratory Press (ISBN: 0-87969-309-6)”
        “Current Protocols in Molecular Biology; edited by Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidmann J. G., Smith A., Struhl K., John Wiley & Sons, Inc. (ISBN: 0-471-50338-X-looseleaf).”

Example of hybridization under medium stringency conditions

    
    


The DNA or RNA is transferred on to a membrane filter (e.g. nylon, nitrocellulose) via Southern Blot or Northern Blot.
The membrane filter containing the target DNA or RNA (e.g. polynucleotide comprising a sequence of SEQ ID NO. 1) is thoroughly wetted in 6×SSC which is prepared from 20×SSC by dilution with water.
(20×SSC: 0,3 M NaCl, 0,3 M Na3-Citrat.2 H2O).
The membrane filter is then prehybridized by adding 0,2 ml prehybridization solution and incubated at 68° C. for 1-2 hours. The prehybridization solution consists of 6×SSC, 5×Denhardt's reagent, 0,5% SDS and 100 μg/ml denatured, fragmented salmon sperm DNA. 5×Denhardt's reagent is prepared from 100×Denhardt's solution by dilution with water.
(100×Denhardt's solution: 10 g Ficoll 400 and 10 g Polyvinylpyrollidone and 10 g Bovine Serum Albumin in 500 ml water).
To the prehybridization mix 10-20 μg/ml of radiolabeled probe (specific activity for example=109 cpm/μg) is added.
If the radiolabeled probe is double stranded, it has to be denatured by heating for 5 min. at 100° C. followed by rapid chilling to between 0° C. to 10° C.
The hybridization mix is incubated for 2 to 14 hours at 60° C. After hybridization the membrane filter is first washed in

    
    
        2×SSC containing 0,5% SDS for 5 minutes at room temperature.
    
    


The filter is then washed in

    
    
        2×SSC containing 0,1% SDS for 15 minutes at room temperature.
    
    


The filter is then washed in

    
    
        0,1% SSC containing 0,5% SDS for 30 minutes at 37° C.
    
    


the filter is then washed in

    
    
        0,1×SSC containing 0,5% SDS for 30 minutes at 42° C.
    
    


After this washing steps the filter is exposed e.g. to X-ray film or is analyzed by a phosphoimager (applied Biosystems).
Example of hybridization under high stringency conditions
The medium and high stringency conditions differ in particular with respect to the temperature and composition of the washing steps. Whereas the prehybridization and incubation with the radiolabeled probe is performed under the same conditions as in case of medium stringent hybridization the washing steps under stringent hybridization are as follows:

    
    
        The membrane filter is first washed in 2×SSC and 0,5% SDS for 5 minutes at room temperature.
        The filter is then washed in 2×SSC containing 0,1% SDS for 30 min at 50° C.
        The filter is then washed in 0,1×SSC containing 0,1% SDS for 30 min at 60° C.
        This last washing step is repeated one more time before the filter is exposed to a X-ray film or analyzed by a phospho imager.
    
    


In another embodiment the invention concerns an isolated polynucleotide comprising a DNA sequence that is selected from one of the following groups

    
    
        a] a DNA sequence of SEQ ID No. 2, 3, 4, 5 or 6; or
        b] a DNA sequence which is complementary to one of the DNA sequences of SEQ ID NO. 2, 3, 4, 5 or 6; or
        c] a DNA sequence which hybridizes to at least one DNA sequence of SEQ ID NO. 2, 3, 4, 5 or 6 or to at least one DNA sequence which is complementary to a DNA sequence of SEQ ID NO. 2, 3, 4, 5 or 6; or
        d] a DNA sequence which is degenerate as a result of the genetic code to at least one DNA sequence of SEQ ID NO. 2, 3, 4, 5 or 6; or
        e] a DNA sequence which is encoding a pak-3b polypeptide.
    
    


In one embodiment of the invention the isolated polynucleotide consists of a polynucleotide sequence of SEQ ID NO. 2, 3, 4, 5 or 6.
In a further embodiment of the invention the pak-3b polypeptide that is encoded by the DNA sequence is the pak-3b polypeptide of C. elegans consisting of an amino acid sequence of SEQ ID NO. 8, 9, 10, 11 or 12.
With respect to the hybridization of a polynucleotide to a pak-3b specifying sequence reference is made to the conditions as drafted aforementioned in context of pak-3a. The conditions as specified for pak-3a are just as applicable for pak-3b.
The invention refers in a further embodiment to a recombinant vector sequence comprising a DNA sequence selected from one of the following groups

    
    
        a] a DNA sequence of one of the SEQ ID NO. 13, 14, 15, 16, 17 or 18; or
        b] a DNA sequence which hybridizes to one of the SEQ ID NO. 13, 14, 15, 16, 17 or 18.
    
    


The conditions for hybridization as specified for pak-3a are applicable for a DNA sequence that hybridizes to one of the SEQ ID NO. 13, 14, 15, 16, 17 or 18 as well.
The invention refers in a further preferred embodiment to a vector sequence that consists of a DNA sequence of one of the SEQ ID NO. 13, 14, 15, 16, 17 or 18.
The invention refers also to a host cell containing a recombinant vector system as specified in SEQ ID NO. 13, 14, 15, 16, 17 or 18.
A host cell may be any cell that is transformable by a vector sequence. Examples of host cells are: Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, insect cells, mammalian cell lines (NIH 3T3; COS; Hela etc.) and others.
A further embodiment of the invention refers to an isolated protein that is encoded by a polynucleotide sequence of SEQ ID NO. 1. This isolated protein can consist of an amino acids sequence of SEQ ID NO. 7. This isolated protein can exhibit the activity of a pak-3a protein.
A further embodiment of the invention refers to an isolated protein that is encoded by a polynucleotide sequence of SEQ ID NO. 2, 3, 4, 5 or 6. Such an isolated protein can consists of an amino acid sequence of SEQ ID NO. 8, 9, 10, 11 or 12. This isolated protein can exhibit the activity of a pak-3b protein.
The invention refers also to the use of a host cell containing a recombinant vector system of SEQ ID NO. 13, 14, 15, 16, 17 or 18 for manufacturing of a protein having an amino acid sequence of SEQ ID NO. 7 and/or exhibiting the activity of a pak-3a protein or for manufacturing of a protein having an amino acid sequence of SEQ ID NO. 8, 9, 10, 11 or 12 and/or exhibiting the activity of a pak-3b protein.
In a further embodiment the invention refers to the use of a host cell containing a recombinant vector system of SEQ ID NO. 13, 14, 15, 16, 17 or 18 in a screening assay for identifying of a compound which interacts with a pak-3a protein or a pak-3b protein. When a compound interacts with a protein in context of the present invention it shall mean that the compound binds to the protein, or that it stimulates the activity of the protein (activation), or it diminishes the activity of the protein (inhibition), or it maintains the activity of the protein, or it stabilizes the acting of the protein.
The invention concerns further the manufacturing of a protein having an amino acid sequence of SEQ ID NO. 7, 8, 9, 10, 11 or 12 and/or exhibiting the activity of a pak-3a or pak-3b protein by cultivation of host cell which harbors a recombination vector sequence of SEQ ID NO. 13, 14, 15, 16, 17 or 18, after cultivation the separation of the cells from cultivation medium, thereafter the lysis of the cells and the purification of the protein by means of protein purification techniques. A person skilled in the art will get access to all required protocols for performing such a method for manufacturing of the protein starting from cultivation of the cells up to the purification of the protein in a text book such as “Current Protocols in Protein Science; edited by Coligan J. E., Dunn B. M., Ploegh H. L., Speicher D. W., Wingfield P. T.; Wiley, John & Sons, Inc. (ISBN: 0471140988)”.
In a further embodiment the invention refers to the use of a protein having an amino acid sequence of SEQ ID NO. 7, 8, 9, 10, 11 or 12 and/or exhibiting the activity of a pak-3a or pak-3b protein to the preparation of an antibody which exhibits binding specificity for such a protein.
In a further embodiment the invention pertains to the use of a protein having an amino acid sequence of SEQ ID NO. 7, 8, 9, 10, 11 or 12 and/or exhibiting the activity of a pak-3a or pak-3b protein the preparation of a medicament for therapy of a disease which is caused by a deficiency, hyperactivation, or malfunction of a mammalian analogous protein of a pak-3a and/or pak-3 protein. Such a mammalian analogous protein may be derived from the human species. It can consist of a kinase protein. The disease involved may be related to a malfunction of the central nervous system, of metabolism, of the cardiovascular system, of the cell division process, or of other cellular or systemic processes.
The invention refers further to the use of a protein having an amino acid sequence of SEQ ID NO. 7, 8, 9, 10, 11 or 12 in a screening process for identifying of a compound that interacts with a pak-3a or a pak-3b protein. Such a screening process can be organized in form of a High-Throughput-Screening (HTS). The HTS is based upon automized screening formats by means of laboratory robot systems.
An embodiment of the invention refers to an assay for identifying of a compound that is interacting with a pak-3a and/or a pak-3b protein wherein

    
    
        a] a pak-3a and/or a pak-3b protein is provided,
        b] a chemical compound is provided,
        c] the pak-3a and/or the pak-3b protein and the chemical compound are brought in contact,
        d] the binding of the chemical compound to the pak-3a and/or pak-3b protein is determined and/or the activity of the pak-3a and/or pak-3b protein is determined.
    
    


The pak-3a or pak-3b protein can consist of a protein having an amino acid sequence of SEQ ID NO. 7, 8, 9, 10, 11 or 12. A chemical compound can be provided by means of a chemical synthesis performed in a chemist's laboratory or by an industrial process. A chemical compound can be further provided by isolation from a biological organism (e.g. bacterium, fungus, plant, mammal etc.).
The pak-3a or pak-3b protein can be provided in form of a host cell which harbors a recombinant vector of SEQ ID NO. 13, 14, 15, 16, 17 or 18 and expresses a protein having the activity of a pak-3a or pak-3b protein. In one embodiment of the invention such a host cell is brought in contact with the chemical compound. In a further embodiment of the invention the assay is used for identifying a compound that is inactivating, or activating, or binding, or maintaining the activity of a pak-3a and/or pak-3b protein.
The invention concerns further a compound that can be identified by such an assay as well as the use of such a compound as pharmaceutically active ingredient or the use of such a compound for manufacturing of a medicament. Such a compound may consist of a molecular weight of 100 to 50 000 kDa.
The invention pertains in a further embodiment to a strain of C. elegans that is exhibiting a loss-of-function phenotype with respect to the pak-3a and/or pak-3b protein. Such a loss-of-function phenotype is detectable by means of southern or northern blots in case the gene and/or the mRNA is not expressed. The loss-of-function phenotype is also detectable by western blots in case the protein is not expressed. The determination of the activity of the pak-3a or pak-3b protein proves the loss-of-function phenotype with respect to the pak-3a and/or pak-3b protein in case the organism is not able to produce functional versions of the proteins, or is degrading the proteins rapidly or contains inhibitors of the proteins.
The loss-of-function phenotype of a C. elegans strains with respect to the pak-3a and/or pak-3b protein can be linked to gonad migration, embryonic lethality or sterility.
In one embodiment of the invention the loss-of-function phenotype of the strain of C. elegans is caused by a mutation or by a partly or complete deletion of the gene coding sequence of pak-3a and/or pak-3b.
In a further embodiment of the invention the loss-of-function phenotype of the strain of C. elegans is causes by an insertion of a polynucleotide sequence into the gene coding sequence of pak-3a and/or pak-3b.
In a further embodiment of the invention the loss-of-function phenotype of the strain of C. elegans is caused by a polynucleotide that is selected from the following group:

    
    
        RNAi; (interference RNA), Ribozyme, antisense RNA, antisense DNA.
    
    


The inactivation of specific mRNAs upon exposure to double-stranded RAN (dsRNA) can in C. elegans be achieved by several different approaches. Below is a short summary of the main approaches.
By feeding
In RNAi by feeding a cDNA or genomic DNA fragment from the gene of interest is cloned in a plasmid between two opposing T7 RNA polymerase promoter sites. The plasmid is subsequently transformed in to an E. coli host strain that contains an inducible T7 RNA polymerase gene and the E. coli strain obtained is used as a C. elegans food source (Timmons and Fire, 1998, Nature, 395, 854; Timmons et al, 2001, Gene 263, 103-112; Kamath et al, 2002, Genome Biology 2, research0002.1-0002.10research0002.1-0002.10).
The advantage of this approach is that relative large numbers of worms can be treated for RNAi and that over several generations. One disadvantage is that some RNAs might be toxic to the E. coli. Normally phenotypes are scored initially in the F1 generation, although some phenotypes occasionally can be observes already in the P0 animals.
By microinjection
The first described approach for RNAi in C. elegans was the microinjection of dsRNA into the animal body cavity (Fire et al, 1998, Nature 391, 801-811). For this approach dsRNA is obtained by in vitro transcription of a cDNA or genomic DNA fragment cloned into a vector with T3, T7 or SP6 RNA polymerase promoter sites, or from a hybrid PCR product containing both suitable RNA polymerase promoter site(s) and sequence from the gene of interest. Normally the two RNA strands are transcribed separately and subsequently annealed together. Alternatively both strands can be transcribed in one reaction (if the insert has been cloned in both orientations downstream of the same promoter), meaning that a separate annealing stap can be left out. The in vitro produced dsRNA is subsequently microinjected into the body of C. elegans animals.
With this approach the number of animals available for analysis is much lower than the feeding method. However, it has occasionally been claimed that microinjection has a higher success rate.
By soaking
Instead of microinjecting the in vitro transcribed dsRNA tha worms can be incubated (“soaked”) in high concentrations of dsRNA (Maeda et al 2001, Current Biology, 11, 171-176).
This approach is less labour intensive than microinjection but is not so commonly used.
By Transgenics
DsRNA can also be produced in situ in the worms by generating transgenic animals expressing either a hairpin RNA molecule that fold on itself to a dsRNA, or by the use of two transgenic constructs expressing the two different RNA strands. Although labour intensive, this approach opens the possibility for stably knocked-down RNAs as well as tissue-specific and inducible RNAi, depending on the promoter chosen for driving the RNA expression (Tavernakis et al, 2000, Nature Genetics, 24, 180-183).
In a further embodiment of the invention the loss-of-function phenotype of the strain of C. elegans is caused by an inhibitor of the pak-3a and/or pak-3b protein.
The invention refers also to the use of a strain of C. elegans that is exhibiting a loss-of-function phenotype for identifying of a protein of the PAK signaling pathway. Such a protein can be a kinase, a phosphates, a transcription enhancer, a transcription repressor or any other protein which is able to interact with a intercellular signaling cascade.
The invention refers further to the use of a strain that is exhibiting a loss-of-function phenotype for identifying a compound that interacts with a protein of the PAK signaling pathway.
The invention further pertains to a method for generating a C. elegans having a phenotype that is characterized by sterility and/or embryonic lethality and/or a defective gonad migration pattern in by

    
    
        a] inactivating the pak-1 gene and/or pak-1 protein in a C. elegans and/or inactivating the pak-3 gene and/or pak-3 protein of the same C. elegans and
        b] identifying of a C. elegans exhibiting the phenotype of sterility and/or embryonic lethality and/or a defective gonad migration pattern.
    
    


In context of this application the term pak-3 shall include pak-3a and pak-3b. When referring to pak-3 the reference shall pertain to pak-3a and/or pak-3b. The inactivating of the pak-1 gene and/or pak-1 protein and pak-3 gene and/or pak-3 protein has to be performed in the same C. elegans organisms. The inactivating of both genes could occur simultaneously at the same time or consecutively one after another. In all cases of inactivation of pak-1 and/or pak-1 to obtain the loss of function phenotype it makes no difference whether the chemical inhibition and/or genetic inactivation of pak-3 is performed before or subsequently after the chemical inhibition and/or genetic inactivation of pak-1.
The identifying of a C. elegans exhibiting the phenotype of sterility and/or embryonic lethality and/or a defective gonad migration pattern can occur in offsprings of the F1 and/or the F2 and/or a further following generation.
The inactivating of the pak-1 gene and/or the pak-1 protein can be achieved by means of RNA molecules that are suitable for RNA interference with a pak-1 coding polynucleotide. Such RNA molecules can be derived from at least one of the vectors of the following group: pKG61 (SEQ ID NO. 26), pKG71 (SEQ ID NO. 28). For that purpose the according vector is introduced into a bacterial strain as e.g. E. coli, the RNA is transcribed from the plasmid promoter and thereafter isolated from the bacteria and purified. The purified RNA is then brought in contact with a cell of C. elegans, or a part of an organism of C. elegans or a complete organism of C. elegans. 
A further possibility of inactivating the pak-1 gene and/or the pak-1 protein consists in feeding bacteria to C. elegans which bacteria contains RNA molecules which are suitable for RNA interference with a pak-1 coding polynucleotide. Such bacteria for the feeding of the C. elegans can harbor at least one plasmid of the following group: pKG61 (SEQ ID NO. 26), pKG71 (SEQ ID NO. 28). The RNA is transcribed from these vectors within the bacteria.
The inactivating of the pak-1 gene and/or the pak-1 protein can be performed by use of a pak-1 knock out strain of C. elegans. Such a knock out strain is e.g. C. elegans RB 689.
The pak-1 gene and/or pak-1 protein can be inactivated by means of an according antisense RNA, antisense DNA, a Ribozyme, an inhibitor of the pak-1 gene transcription or an inhibitor of the pak-1 protein.
The inactivating of the pak-3 gene and/or pak-3 protein can be achieved by means of RNA molecules that are suitable for RNA interference with a pak-3 coding polynucleotide. Such RNA molecules can be derived from at least one of the vectors of the following group: pKG65 (SEQ ID NO. 27), pKG71 (SEQ ID NO. 28), pKG63 (SEQ ID NO. 29), pKG64 (SEQ ID NO. 30). For that purpose the according vector is introduced into a bacterial stain as e.g. E. coli, the RNA transcribed from the plasmid promoter and thereafter isolated from the bacteria and purified. The purified RNA is then brought in contact with a cell of C. elegans, or part of an organism of C. elegans or a complete organism of C. elegans. A further possibility of inactivating the pak-3 gene and/or the pak-3 protein consists in feeding to C. elegans which bacteria contain RNA molecules which are suitable for RNA interference with a pak-3 coding polynucleotide. Such bacteria for the feeding of the C. elegans can harbor at least one plasmid of the following group: pKG65 (SEQ ID NO. 27), pKG71 (SEQ ID NO. 28), pKG63 (SEQ ID NO. 29), pKG64 (SEQ ID NO. 30). The RNA is transcribed from these vectors within the bacteria. The inactivating of the pak-3 gene and/or pak-3 protein can be performed by use of a pak-3 knock out strain of C. elegans. The pak-3 gene and/or pak-3 protein can be inactivated by means of an according antisense RNA, antisense DNA, a Ribozyme, an inhibitor of the pak-3 gene transcription or an inhibitor of the pak-3 protein.
The invention pertains further to a strain of C. elegans which is characterized by a phenotype of sterility and/or embryonic lethality and/or a defective gonad migration and which harbors an inquired or missing pak-1 function and an impaired or missing pak-3 function. In context of this application the term function shall refer to the gene and/or the protein. The strain of C. elegans of the invention which is characterized by a phenotype of sterility and/or embryonic lethality and/or a defective gonad migration pattern could be obtainable or could be obtained by one or several of the methods for generating a C. elegans having said phenotypes. Such a strain can be used amongst other things for characterizing the intercellular signaling cascade linked to pak-1 and/or pak-3. Such a strain can also be used for identifying of a compound that interferes with one or several proteins which are part of the signaling cascade linked to pak-1 and/or pak-3. Such a strain can further be used for identification of a compound that interferes with transcription of one or several proteins that are part of the signaling cascade linked to pak-1 and/or pak-3.
The invention relates also to manufacturing of a RNA molecule wherein at least one of the polynucleotides of pKG61 (SEQ ID NO. 26), pKG65 (SEQ ID NO. 27), pKG71 (SEQ ID NO. 28), pKG63 (SEQ ID NO. 29), pKG64 (SEQ ID NO. 30), pKG167 (SEQ ID NO. 31) or pKG168 (SEQ ID NO. 32) is transformed into a bacterial strain, the RNA is transcribed from the vector and the transcribed RNA is isolated and/or purified. The invention pertains also to RNA molecules that are obtainable or obtained by such a method. These RNA molecules can be used as individual species one by one or in a combined manner for RNA interference with a pak-1 and/or pak-3 protein coding polynucleotide.
DESCRIPTION OF SEQ IDS
SEQ ID NO. 1 is disclosing the polynucleotide sequence of the pak-3 cDNA. The pak-3a gene is consisting of the coding information of a kinase domain.
SEQ ID NO. 2 is disclosing the polynucleotide sequence of the pak-3b cDNA. The pak-3b gene is consisting of the coding information of a kinase domain of the same sequence composition as pak-3a and a additional CRIB domain (cdc42/Rac interactive binding domain) which is 5′-linked to the kinase domain.
SEQ ID NO. 3 is disclosing the polynucleotide sequence of the pak-3b cDNA harboring a silent polymorphism (change from gct to gcc) that would leave the concerned Ala of the corresponding protein unchanged.
SEQ ID NO. 4 is disclosing the polynucleotide sequence of the pak-3b cDNA harboring the silent polymorphism as described in SEQ ID NO. 3 and harboring further a in frame 6 bp insertion within the kinase domain.
SEQ ID NO. 5 is disclosing the polynucleotide sequence of the pak-3b cDNA harboring an in frame 9 bp insert within the CRIB domain and having the corresponding sequence of Exon 7 deleted.
SEQ ID NO. 6 is disclosing the polynucleotide sequence of the pak-3b cDNA harboring a polymorphism (change from atc to gtc) within the CRIB domain which changes an Ile into a Val of the corresponding protein and harboring the in frame insertion of 6 bp of the kinase domain (as is the same as in SEQ ID NO. 4).
SEQ ID NO. 7 is disclosing the amino acid sequence of the corresponding protein of SEQ ID NO. 1 (kinase domain).
SEQ ID NO. 8 is disclosing the amino acid sequence of the corresponding protein of SEQ ID NO. 2 (kinase domain plus CRIB domain).
SEQ ID NO. 9 is disclosing the amino acid sequence of the corresponding protein of SEQ ID NO. 3 (kinase domain plus CRIB domain).
SEQ ID NO. 10 is disclosing the amino acid sequence of the corresponding protein of SEQ ID NO. 4 (kinase domain having a 6 bp insert plus CRIB domain).
SEQ ID NO. 11 is disclosing the amino acid sequence of the corresponding protein of SEQ ID NO. 5 (kinase domain plus CRIB domain having a 9 bp insert and Exon 7 deleted).
SEQ ID NO. 12 is disclosing the amino acid sequence of the corresponding protein of SEQ ID NO. 6 (kinase domain having a 6 bp insert plus CRIB domain in which Ile is changed into a Val).
SEQ ID NO. 13 is disclosing the polynucleotide sequence of vector pKG40, which is encompassing the polynucleotide sequence of SEQ ID NO. 1. A description of the vector is given within the header of FIG. 13.
SEQ ID NO. 14 is disclosing the polynucleotide sequence of vector pKG 123, which is encompassing the polynucleotide sequence of SEQ ID NO. 2. A description of the vector is given within the header of FIG. 14.
SEQ ID NO. 15 is disclosing the polynucleotide sequence of vector pKG 43, which is encompassing the polynucleotide sequence of SEQ ID NO. 3. A description of the vector is given within the header of FIG. 15.
SEQ ID NO. 16 is disclosing the polynucleotide sequence of vector pKG 44, which is encompassing the polynucleotide sequence of SEQ ID NO. 4. A description of the vector is given within the header of FIG. 16.
SEQ ID NO. 17 is disclosing the polynucleotide sequence of vector pKG 58, which is encompassing the polynucleotide sequence of SEQ ID NO. 5. A description of the vector is given within the header of FIG. 17.
SEQ ID NO. 18 is disclosing the polynucleotide sequence of vector pKG 59, which is encompassing the polynucleotide sequence of SEQ ID NO. 6. A description of the vector is given within the header of FIG. 18.
SEQ ID NO. 19 is disclosing the primer sequence kg 1.
SEQ ID NO. 20 is disclosing the primer sequence kg 2.
SEQ ID NO. 21 is disclosing the primer sequence kg 25.
SEQ ID NO. 22 is disclosing the primer sequence kg 26.
SEQ ID NO. 23 is disclosing the primer sequence kg 37.
SEQ ID NO. 24 is disclosing the primer sequence kg 27.
SEQ ID NO. 25 is disclosing the primer sequence kg 50.
SEQ ID NO. 26 is disclosing the polynucleotide sequence of vector pkG61/dT7-pak-1. A description of the vector is given within the header of FIG. 26.
SEQ ID NO. 27 is disclosing the polynucleotide sequence of vector pkG65/dT7-pak-3 . A description of the vector is given within the header of FIG. 27.
SEQ ID NO. 28 is disclosing the polynucleotide sequence of vector pkG 71/dT7-pak-3/pak-1. A description of the vector is given within the header of FIG. 28.
SEQ ID NO. 29 is disclosing the polynucleotide sequence of vector pkG63/dT7-pak-3a. A description of the vector is given within the header of FIG. 29.
SEQ ID NO. 30 is disclosing the polynucleotide sequence of vector pkG64/dT7-pak-3b. A description of the vector is given within the header of FIG. 30.
SEQ ID NO. 31 is disclosing the polynucleotide sequence of vector pkG167/dT7-ced-10. A description of the vector is given within the header of FIG. 31.
SEQ ID NO. 32 is disclosing the polynucleotide sequence of vector pkG168/dT7-mig-2. A description of the vector is given within the header of FIG. 32.
SEQ ID NO. 33 is disclosing the polynucleotide sequence of expressed sequence tag (EST) y38f1a.10 of C. elegans. 
SEQ ID NO. 34 is disclosing the polynucleotide sequence of EST yk65141 5′ of C. elegans. 
SEQ ID NO. 35 is disclosing the polynucleotide sequence of EST yk65141 3′ of C. elegans. 
SEQ ID NO. 36 is disclosing the polynucleotide sequence of EST F18a 11.4 of C. elegans.



DESCRIPTION OF THE FIGURES
FIG. 1 exhibits SEQ ID NO. 1.
FIG. 2 exhibits SEQ ID NO. 2.
FIG. 3 exhibits SEQ ID NO. 3.
FIG. 4 exhibits SEQ ID NO. 4.
FIG. 5 exhibits SEQ ID NO. 5.
FIG. 6 exhibits SEQ ID NO. 6.
FIG. 7 exhibits SEQ ID NO. 7.
FIG. 8 exhibits SEQ ID NO. 8.
FIG. 9 exhibits SEQ ID NO. 9.
FIG. 10 exhibits SEQ ID NO. 10.
FIG. 11 exhibits SEQ ID NO. 11.
FIG. 12 exhibits SEQ ID NO. 12.
FIG. 13A and B exhibits SEQ ID NO. 13.
FIG. 14A and B exhibits SEQ ID NO. 14.
FIG. 15A and B exhibits SEQ ID NO. 15.
FIG. 16A and B exhibits SEQ ID NO. 16.
FIG. 17A and B exhibits SEQ ID NO. 17.
FIG 18A and B exhibits SEQ ID NO. 18.
FIG. 19 exhibits SEQ ID NO. 19.
FIG. 20 exhibits SEQ ID NO. 20.
FIG. 21 exhibits SEQ ID NO. 21.
FIG. 22 exhibits SEQ ID NO. 22.
FIG. 23 exhibits SEQ ID NO. 23.
FIG. 24 exhibits SEQ ID NO. 24.
FIG. 25 exhibits SEQ ID NO. 25.
FIG. 26A and B exhibits SEQ ID NO. 26.
FIG. 27A and B exhibits SEQ ID NO. 27.
FIG. 28A and B exhibits SEQ ID NO. 28.
FIG. 29A and B exhibits SEQ ID NO. 29.
FIG. 30A and B exhibits SEQ ID NO. 30.
FIG. 31A and B exhibits SEQ ID NO. 31.
FIG. 32A and B exhibits SEQ ID NO. 32.
FIG. 33 exhibits SEQ ID NO. 33.
FIG. 34 exhibits SEQ ID NO. 34.
FIG. 35 exhibits SEQ ID NO. 35.
FIG. 36 exhibits SEQ ID NO. 36.
FIG. 37 Gonad path finding phenotypes (A) and intensing of gonad defects.










Abbreviations
















NGM
Nematode growing medium


E. coli OP50
Uracil requiring strain of E. coli; used as a food source



for nematodes


DMSO
Dimethylsulfoxide.












Deposit of plasmid DNA
The plasmids of the present invention have been deposited with the DSMZ—Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

    (German Collection of Microorganisms and Cell Cultures GmbH)
    Mascheroder Weg 1 b
    D-38124 Braunschweig
    according to the following numbers:
    
        plasmid pKG40=DSM 16147 (see also SEQ ID NO. 13 as well as FIG. 13)
        plasmid pKG43=DSM 16148 (see also SEQ ID NO. 15 as well as FIG. 15)
        plasmid pKG44=DSM 16149 (see also SEQ ID NO. 16 as well as FIG. 16)
        plasmid pKG58=DSM 16150 (see also SEQ ID NO. 17 as well as FIG. 17)
        plasmid pKG59=DSM 16151 (see also SEQ ID NO. 18 as well as FIG. 18)
        plasmid pKG123=DSM 16152 (see also SEQ ID NO. 14 as well as FIG. 14)
    
    


EXAMPLES
Strains, general strain culture, molecular & genetic methods
Nematode culture was done according to Brenner 1974.
Strains were obtained from the C. elegans Genomics Center (CGC) and the C. elegans knock out consortium.
Cloning of pak-3
The different isoforms of pak-3 cDNA were cloned by RT-PCR from N2 (C. elegans wild-type) total RNA. All primers contain 5′adaptor sequences to allow Gateway cloning. RT-PCR products with 5′ Gateway adaptor sequences were re-amplified using AttB sequence primers







(SEQ ID NO. 19)









kg1; GGGGACAAGTTTGTACAAAAAAGCAGGCT,



 







(SEQ ID NO. 20)









kg2; GGGGACCACTTTGTACAAGAAAGCTGGGT,






and cloned via the BP reaction into the vector pDONR201 as described by the manufacturer (Invitrogen).

Sequence alignments were done using the Lasergene software package. Blast database searches were conducted using the NCBI Blast tool (internal installation). Sequence motifs were identified using the Workbench Pfam HMM database search tool (GeneData AG).
pKG40 (pak-3a wild-type; DSM 16147) was cloned by the use of gene-specific primers based on the gene prediction for y38f1a.10, (SEQ ID NO. 33). (5′: kg25; aaaaagcaggctcaaaaATGTTTCAAAATAGTCCGATGAT (SEQ ID NO. 21; 3′: kg26; agaaagctgggtCTACTTTTCTCGGACGGCTCT, SEQ ID NO. 22). (One pak-3a clone was isolated by the 5′ SL1 primer kg37 [see below] in combination with kg26. This clone was found to have an ORF identical to pKG40 and was not kept).
pKG43 (pak-3b SL 1 t1680c; Ala-Ala; DSM 16148) was cloned by a 5′ primer corresponding to the SL1 trans-spliced leader sequence (kg37; aaaaagcaggctGGTTTAATTACCCAAGTTTGAG, SEQ ID NO. 23) in conjunction with the 3′ primer kg26 (agaaagctgggtcTACTTTTCTCGGACGGCTCT, SEQ ID NO. 24).
pKG44 (pak-3b Ins1581 t1686c; DSM 16149), pKG58 (pak-3b Ins228 Deta Exon 7) and pKG59 (pak-3b a43g Ins1581) were all cloned by combining a gene-specific 5′ primer, kg50 (aaaaagcaggctcaaaaATGTCAACTTCAAAAAGTTCCAAG, SEQ ID NO. 25), derived from the sequence information from pKG43, with the 3′ primer kg26 (SEQ ID NO. 22).
pKG123 (pak-3b wild-type; DSM 16152) was constructed by replacing an EcoRV-Sacl restriction fragment (the C-terminal part of the kinase domain) in pKG44, containing deviations from the wild-type sequence, with the corresponding wild-type fragment from pKG58, thus creating a full-length, wild-type cDNA clone.
RNAi
RNA interference was done using the feeding method as described previously in Fraser et al. 2000 and Kamath et al. 2000. Double RNAi was done either by mixing bacterial cultures before seeding plates or by generation of vector constructs containing two cDNA fragments.
Vectors for RNAi by feeding were generated by cloning full-length or partial cDNAs into derivatives of the double T7 vector pPD129.36 (Timmons & Fire, Nature 395, 854). Either a Gateway-adopted version (pKG14) was used for cloning according to standard Gateway protocols (Invitrogen) or a version with a Srfl site added to the polylinker (pKG90) was used for direct cloning of PCR products as described (Schlotterer, C. and Wolff, C. Trends Genet, 1996. 12, 286-287).
RNAi vectors:

    
    
        pKG61 (dT7-pak-1); vector; pKG14; insert: bp 1-1710 of pak-1; the RNA is encoded from 89 to 1753 of SEQ ID NO. 26 (entire ORF) (SEQ ID NO. 26)
        pKG65 (dT7-pak-3); vector: pKG14; insert: bp 1141-1941 of pak-3b (kinase domain); the RNA is encoded from 84 to 883 of SEQ ID NO. 27; specific for both pak-3a and pak-3b (SEQ ID NO. 27)
        pKG71 (dT7-pak-3/-1); vector pKG14; inserts: bp 1141-1941 of pak-3b (kinase domain) and bp 921-1710 of pak-1 (kinase domain); the RNA is encoded from 84 to 884 (pak1) and 885 to 1674 (pak3) of SEQ ID NO. 28; for double RNAi against pak-1/pak-3 (SEQ ID NO. 28)
        pKG63 (dT7-pak-3a); vector pKG14; insert: bp 1-128 of pak-3a (N-terminus); the RNA is encoded from 89 to 216 of SEQ ID NO. 29; specific for pak-3a (SEQ ID NO. 29)
        pKG64 (dT7-pak-3b); vector pKG14; insert: bp 1-788 of pak-3b (N-terminus); the RNA is encoded from 89 to 876 of SEQ ID NO. 30; specific for pak-3b (SEQ ID NO. 30)
        pKG167 (dT7-ced-10); vector pKG90; insert: bp 40-562 of c09g12.8 b (ced-10); the RNA is encoded from 136 to 658 of SEQ ID NO. 31
        pKG169 (d7-mig-2); vector pKG90; insert: bp 13-566 of c35c5.4 (mig-2); the RNA is encoded from 137 to 689 of SEQ ID NO. 32.

Assay for phenotypic analysis

    
    


Egg lay was scored by placing 5 or 10 [for 1. pak-1(RNAi); 2. pak-1(ok448); pak-3(RNAi) 3. pak-1(ok448); pak-3b(RNAi)] adult F1 generation worms (1st generation progeny from the P0 parents initially exposed to RNAi treatment) on plates (5 plates per RNAi treatment) for 5 h at 20° C. and subsequence manual counting of the eggs after removal of the adult worms. Embryonic lethality was defined as the number of eggs remaining 24 h after removal of the adult worms relative the total number of eggs laid.
Gonad morphology and distal tip cell (DTC) migration was scored essentially as described previously (Nishiwaki 1999 Genetics 152, 985-997; Su et al 2000, Development 127, 585-594). Briefly, F1 generation late L4 larvae or young adults were observed under Nomarski (DIC) optics using an Axioplan 2 microscope (Sulston and Horwitz 1977, Dev Biol 56, 110-156) and the trajectories of the DTCs were deduced from the shapes of the gonad arms. As a negative control worms were exposed to bacteria expressing the empty T7 vector. The DTC migration phenotypes were group into five different classes (FIG. 1a): I) wild-types, showing the typical C-shaped gonad with normal 1st and 2nd turns; II) Rac-type, typically observed in ced-10 and mig-2 mutants, with normal 1st and 2nd turns but with an additional 3rd turn leading to that the gonadal tip points away from the midbody region (Reddien and Horwitz 2000, Nature Cell Biol 2, 131-136); III) Pak-type, with a normal 1st turn but a 2nd turn in the wrong direction away from the midbody region (a similar phenotype has been described previously for the mutant mig-14 [Nishiwaki 1999]); IV) Straight, where the gonad progresses without any turns along the ventral side away from the midbody region; V) Other, mainly a complete lack of gonad outgrowth or ruptured gonads with free-floating germ cells in the body.
Compound testing
For screening of candidate pak-3 inhibitory compounds, synchronized RB689 (pak-1, ok448) L1 larvae were obtained by NaOH/Na-hypochlorite treatment of gravid adults and subsequent incubation of the resulting eggs in M9 buffer O/N at 20° C. with agitation essentially as described (C. elegans, a practical approach, Ed. I. Hope, 1999). About 30 L1 larvae in NGM medium were mixed with 2 OD600 E. coli OP-50, 100 μM test compound, 1% DMSO (from compound stock solution) in a final volume of 50 μl per well in flat-bottomed 96-well plates and incubated at 20° for 3 to 4 days. Preliminary in-well scoring of gonad phenotypes was done using an Axiovert 200 microscope. For final scoring, worms were pipetted out of the wells, mounted and analyzed under Nomarski (DIC) optics. As a negative control worms were incubated with 1% DMSO.
Cloning of pak-3 cDNAs and identification of the pak-3 gene
The initial indication of a hitherto unknown pak gene in C. elegans came from the identification of a predicted open reading frame, y38f1a.10 (SEQ ID NO. 33), encoding a kinase domain with high homology to a pak-type kinase domain. (The kinase domain is also classified as a pak-type kinase domain in the kinase database “kinase.com” located on the world wide web). However, the predicted ORF y38f1a.10 does not encode for a CRIB-domain, the regulatory domain conserved within the PAK gene family. We noticed by sequence comparison that the EST yk651h1 (SEQ ID NO. 34, 35), covering the y38f1a.10 ORF, also contains parts of the predicted ORF f18a11.4 (SEQ ID NO. 36), located upstream of y38f1a.10. This suggested to us that those two predicted ORFs might in fact be one single gene. To test this we performed RT-PCR using a 3′ gene-specific primer corresponding to the 3′ end of y38f1a.10 and a 5′ primer corresponding to the SL1 leader sequence spliced in trans to many C. elegans mRNAs. As it has been reported that the C. elegans pak-1 mRNA is SL1 trans-spliced we suspected that this might be the case also for mRNAs from other C. elegans pak genes.
Sequence analysis of the RT-PCR products obtained revealed two different classes of mRNAs. The first class (isoforms a) corresponds roughly to the predicted ORF y38f1a.10 but with an additional exon upstream of the kinase domain. The second class (isoforms b) spans both ORFs y38f1a.10 and f18a11.4, thus demonstrating that these two ORFs belong to one single gene. However, the mRNAs have a 5′ region longer than predicted in f18a11.4 and also longer than the EST yk651h1. Sequence analysis revealed a splicing pattern different from the ORF f18a11.4 and most importantly a domain with homology by a CRIB domain. Blast sequence database searches with cDNA isoforms b yielded a highest similarity score against human and rodent PAK3 and secondly against human and rodent PAK1.
Taken together this demonstrates that the two predicted ORFs y38f1a.10 (SEQ ID NO. 33) and f18a.11.4 (SEQ ID NO. 36) are in fact one gene that codes for two different mRNA splice variants, a short form encoding a protein mainly consisting of a pak-type kinase domain and a 5′ longer form encoding a typical PAK protein. Based on sequence similarity and biological function (see below) we propose to call this novel pak gene pak-3 with the short splice variant denoted pak-3a and the long form pak-3b.
RNAi in C. elegans strains N2 (wild type) and RB689 (pak-1)
To assess the biological function of pak-3, RNAi by feeding experiments were performed. However, no obvious phenotypes could be detected when N2 wild-type worms were used for RNAi. Similarly, no phenotypes were observed when pak-1 function was assayed by RNAi, which was corroborated by observation of the pak-1 knock-out strain RB689, appearing completely wild-type in morphology and behavior.
Based on the similarity between pak-1 and pak-3 it was concluded that the lack of phenotypes in the RNAi experiments could be explained by supplementary functions of pak-1 and pak-3. To confirm this double RNAi experiments were conducted in the N2 background as well as pak-3 RNAi in the pak-1 knock-out strain RB689 (ok448). Similar results were obtained in both approaches, showing several drastic phenotypes: sterility, embryonic lethality and defects in the gonad migration pattern. Sterility was not completely penetrate but reproducibly shown to be very strong and readily visible. The result of a representative quantitative experiment is shown in Table I. Compared to the control worms exposed to mock RNAi treatment, the relative number of eggs laid by animals exposed to pak-1; pak-3 double RNAi was only 17%, when double RNAi was performed by mixing pak-1 and pak-3 RNAi bacterial cultures. When double RNAi was done using bacteria expressing a hybrid pak-1/pak-3 double RNA molecule the effect was somewhat stronger, 11%, suggesting that double RNAi by mixing of cultures is only moderately less efficient then the use of a dedicated double RNAi vector.
In pak-1lg (ok448); pak-3 (RNAi) animals sterility was even more penetrant, only 3% compared to pak-1lf (ok 448); mock (RNAi). When compared with the results obtained in the N2 background, this indicates that pak-1 RNAi is not as penetrant as the complete knock-out, which can be expected.
Embryonic lethality was initially observed from the presence of small, round eggs that did not hatch upon prolonged incubation. Closer examination of these eggs suggested a high degree of cellular differentiation, for example muscle and pharynx tissue was clearly present. However, the overall morphology of the embryos was distorted, ranging from moderate to very severe with no morphological features conserved. A quantitative analysis (Table I) demonstrated more than 20% embryonic lethality in N2 animals and almost 40% in the RB689 background.
Interestingly, the phenotypes could not be observed in the first generation (P0) of worms exposed to RNAi, sterility and gonad defects were first observed in the F1 generation. Embryonic lethality was first seen in F2 generation embryos, suggesting material rescue in the F1 generation.
The cloning of pak-3 cDNAs had revealed the existence of two different splice variants, pak-3a and pak-3b. The functional importance of the two forms was demonstrated by conducting isoforms-specific RNAi in the RB689 background. Both as assayed from the sterility phenotype and as well as embryonic lethality it appears that the longer isoform pak-3b may play the mayor role with respect to the phenotypes observed (Table I).
A third pak gene is encoded by the predicted gene c 45b11.1, which is most similar to the human PAK4. It is known that mammalian PAK4 differ significantly in regulation and function from PAK1 and PAK3. In agreement with this, no additional phenotypes were observed in double RNAi experiments between c45b11.1 and pak-1 or pak-3.
pak-3 and pak-1 are required for DTC pathfinding
In the C. elegans hermaphrodite the shape of the bi-lobed gonad is determined by the paths of cell migration of the gonadal distal tip cells (DTCs). In wild-type animals the two gonadal arms develop from the ventrally located gonadal primordium in the midbody. One DTC migrates anteriorly and the other posteriorly close to the ventral midline. The migration of the DTCs then undergoes two turns, the first turn towards the dorsal side and the second turn towards the midbody. The result of these migrations is the formation of the two symmetrical C-shaped adult gonad arms. As mentioned above we noted deviations from the wild-type gonad shape, indicative of defects in DTC migration, were noted in pak-3(RNAi); pak-1(RNAi) and pak-3(RNAi); RB689(ok448) animals, but not in single pak-3(RNAi); pak-1(RNAi) or the RB689 strain itself. Thus, also for this phenotype pak-1 and pak-3 appears to act supplementary. In more than half of the of gonads observed the first turn appeared normal whereas the second turn was in the wrong direction, i.e. instead of turning towards the midbody, the posterior gonad continued posteriorly and the anterior continued anteriorly (FIG. 1). Occasionally gonads without any turns were observed, the gonads continuing along the ventral midline towards the posterior and anterior end of the animal, respectively.
There were also analyzed the pak-3 isoform specific effects on DTC migration by pak-3b and pak-3a RNAi in the RB689 background. The results demonstrate that only the pak-3b isoform is important for DTC information, as for the sterility and embryonic lethality phenotypes (Table II).
Pak-Rac interaction
It has previously been described that two of the three Rac GTPases in C. elegans, ced-10 and mig-2, are involved in DTC pathfinding (Reedien & Horwitz, 2000, Lundquist et al 2001). In ced-10 and mig-2 mutants the gonads undergo a third, extra, turn after the second turn, leading to gonad tips pointing away from the midbody. This phenotype is different from what was observed in pak-1; pak-3 mutant animals, in which already the second turn was defective. It is furthermore known from invitro studies and mammalian cell systems (e.g. Bishop & Hall Biochem J, 2000) that Rho GTPases, to which the Rac proteins belong, are upstream regulators of PAKs. Given that the C. elegans paks also are important for DTC pathfinding it was deducted that there is an interaction between pak-1 and pak-3 and the two Racs ced-10 and mig-2 in C. elegans gonad development. To demonstrate this a set of RNAi experiments was performed in different genetic backgrounds (summarized in Table II). The different experimental combinations consistently showed that mig-2 or ced-10 loss of function did not lead to a stronger phenotype in combination with pak-3 than the separate single loss of function mutants. However, in combination with pak-1 mutants the penetrance and severity of the gonad migration defects increased dramatically. As pak-1 and pak-3 act supplementary, these results suggest that ced-10 and mig-2 act as upstream regulators of pak-3 but not, or only to a minor extent, of pak-1. Interestingly, the ced-10; mig-2; pak-1 triple mutant animals were much stronger affected than pak-1; pak-3 double mutants, suggesting that the two Racs also act through other pathways than pak-3 in parallel. Furthermore it was not only observed that the penetrance of DTC pathfinding defects was higher in ced-10; mig-2; pak-1 animals but also the phenotypic spectrum shifted towards more severe pathfinding and migration defects. High frequencies of gonads were observed without turns and also gonad movement defects. This demonstrates that both Paks and Racs are involved in several stages and aspects of DTC pathfinding but that these functions are not evident in the single or double mutants, probably as an effect of the redundant functions of these genes.
Compound mimicking RNAi phenotype
To investigate if the gonad migration defect phenotype can be used as a reporter for PAK-3 inhibitory small molecules, worms were exposed to a set of potential PAK inhibitors, derived from a chemical compound collection, in a 96-well assay format. Synchronized RB689 (pak-1, ok448) L1 larvae were incubated with test compounds in NGM (media) and E. coli OP-50 as food source. As the compounds were added as DMSO solutions, worms exposed to DMSO was used as a control. At late L4 or early young adult stage, gonad phenotypes were scored.
Several of the 14 substances tested showed a partial effect on gonad migration, causing phenotypes similar to those seen in pak-1; pak-3 (RNAi) animals. In particular, one compound tested, A000025706, was shown to reproducibly cause gonad migration defects (Table III). Out of 100 gonads analyzed, 74 were found to have gonad migration defects.
The observation that the types of defects observed differ somewhat from those observed with RNAi is possibly due to phamacological properties of the compound, e.g. uptake and stability. It is also possible that other kinases involved in gonad development and other developmental processes are also inhibited by A000025706. In fact, we observed general growth retardation in worms treated with this compound, suggesting a certain degree of non-specified effects of A000025706. However, as A000025706 has been confirmed as a PAK inhibitor in other assays (data not shown) we believe that most or all of the gonad migration defects observed can be attributed to a specific inhibition of PAK-3.
The observation that PAK inhibitors can be identified in a C. elegans-based assay demonstrates the usefulness of the model organism as a tool for phamacological research. The fact that growth retardation was observed also exemplified that potential side effects can be identified in parallel to the specific assay readout, i.e. that C. elegans-based assays can be valuable as high-throughput screening systems.











TABLE I









% Emb


Strain
RNAi treatment
Genotype
% Eggs laid
Lethality



















N2
ctrl
Wild-type
100
0.2



pak-1
pak-1 (RNAi)
113
2.2



pak-3
pak-3 (RNAi)
69
5.0



pak-1/-3 (one vector
pak-1 (RNAi);
11
20.8




pak-3(RNAi);



pak-1/pak-3
pak-1(RNAi);
17
15.4



(mixed vectors)
pak-3(RNAi


RB689
ctrl
pak-1(ok448)
100
4.4



pak-3
pak-1(ok448);
3
38.7




pak-3(RNAi)



pak-3a
pak-1(ok448);
134
4.0




pak-3a(RNAi)



pak-3b
pak-1(ok448);
2
22.7




pak-3b(RNAi





















TABLE II










movement





pathfinding defects
defects
% affected
















Strain
RNAi construct
Genotype
% wt
% rac
% pak
% straight
% other
gonads
n



















N2
ctrl
Wild type
100.0
0.0
0.0
0.0
0.0
0.0
168



pak-1
pak-1(RNAi)
100.0
0.0
0.0
0.0
0.0
0.0
154



pak-3
pak-3(RNAi)
99.3
0.0
0.0
0.7
0.0
0.7
150



pak-1/-3(one vector)
pak-1(RNAi); pak-3(RNAi)
41.7
0.0
54.3
3.5
0.4
58.3
230



pak-1/pak-3(mixed
pak-1(RNAi); pak-3(RNAi)
44.6
0.0
52.2
3.3
0.0
55.4
92



vectors)



mig-2
mig-2(RNAi)
91.2
8.1
0.7
0.0
0.0
8.8
136



mig-2/pak-1
mig-2(RNAi); pak-1(RNAi)
75.0
1.6
22.6
0.8
0.0
25.0
124



mig-2/pak-3
mig-2(RNAi); pak-3(RNAi)
88.8
7.2
2.0
2.0
0.0
11.2
152



mig-2/ced-10
mig-2(RNAi); ced-10(RNAi)
92.7
5.6
1.6
0.0
0.0
7.3
124



ced-10
ced-10(RNAi)
90.5
8.8
0.7
0.0
0.0
9.5
148



ced-10/pak-1
ced-10(RNAi); pak-1(RNAi)
49.2
1.6
36.7
12.5
0.0
50.8
128



ced-10/pak-3
ced-10(RNAi); pak-3(RNAi)
96.6
3.4
0.0
0.0
0.0
3.4
146


RB689
ctrl
pak-1(ok448)
99.5
0.0
0.5
0.0
0.0
0.5
198


pak


1(ok448)



pak-3
pak-1(ok448); pak-3(RNAi)
44.1
0.0
49.6
4.7
1.7
55.9
236



pak-3a
pak-1(ok448); pak-3a(RNAi)
100.0
0.0
0.0
0.0
0.0
0.0
80



pak-3b
pak-1(ok448); pak-3b(RNAi)
31.7
0.0
54.9
2.4
11.0
68.3
82



mig-2
pak-1(ok448); mig-2(RNAi)
55.6
0.0
33.8
10.6
0.0
44.4
160



mig-2/pak-3
pak-1(ok448); pak-3(RNAi);
57.8
0.0
24.7
16.9
0.6
42.2
154




mig-2(RNAi)



mig-2/ced-10
pak-1(ok448); mig-2(RNAi);
29.8
0.0
13.7
55.6
0.8
70.2
124




ced-10(RNAi)



ced-10
pak-1(ok448); ced-10(RNAi)
37.8
1.2
32.3
28.0
0.6
62.2
164



ced-10/pak-3
pak-1(ok448); pak-3(RNAi);
43.8
3.1
34.6
18.5
0.0
56.2
162



pak-1
pak-1(RNAi); mig-2(mu28)
40.5
3.2
43.7
9.5
3.2
59.5
126



pak-3
pak-3(RNAi); mig-2(mu28)
74.6
23.0
0.0
2.4
0.0
25.4
126



pak-1/-3
pak-1(RNAi); pak-3(RNAi);
5.5
0.8
43.0
48.4
2.3
94.5
128




mig-2(mu28)



mig-2
mig-2(mu28); mig-2(RNAi)
65.9
34.1
0.0
0.0
0.0
34.1
88



ced-10
mig-2(mu28); ced-10(RNAi)
59.8
14.8
13.9
7.4
4.1
40.2
122



ced-10/pak-1
pak-1(RNAi); mig-2(mu28);
14.1
4.7
20.3
50.0
10.9
85.9
128




ced-10(RNAi)



ced-10/pak-3
pak-3(RNAi); mig-2(mu28);
74.6
14.8
4.1
2.5
4.1
25.4
122




ced-10(RNAi)


MT5013
ctrl
ced-10(n1993)
77.3
21.4
0.0
0.6
0.6
22.7
154


ced-10


(n1993)



pak-1
pak-1(RNAi); ced-10(n1993)
47.4
1.3
36.4
14.3
0.6
52.6
154



pak-3
pak-3(RNAi); cad-10(n1993)
82.5
14.3
1.3
1.3
0.6
17.5
154



pak-1/-3
pak-1(RNAi); pak-3(RNAi);
49.7
0.7
43.0
2.6
4.0
50.3
151




ced-10(n1993)



mig-2
mig-2(RNAi); ced-10(n1993)
81.7
6.3
4.8
1.6
5.6
18.3
126



mig-2/pak-1
pak-1(RNAi); mig-2(RNAi);
11.3
2.4
16.1
50.8
19.4
88.7
124




ced-10(n1993)



mig-2/pak-3
pak-3(RNAi); mig-2(RNAi);
87.1
8.9
0.0
0.0
4.0
12.9
124




ced-10(n1993)



ced-10
ced-10(n1993); ced-10(RNAi)
75.0
9.2
5.3
0.0
10.5
25.0
76























TABLE III





Strain
Cpd
% wt
% pak-like
% Straight
% Movement Def
% affected
n






















RB689 pak-1(ok448)
ctrl
99
0
0
1
1
80


RB689 pak-1(ok448)
25706
26
4
51
19
74
100

## Claims

1. An isolated polynucleotide comprising a DNA sequence selected from one of the following groups:
a] a DNA sequence of SEQ ID NO. 1; or
b] a DNA sequence which is complementary to SEQ ID NO. 1; or
c] a DNA sequence which is degenerate as a result of the genetic code to the DNA sequence of SEQ ID NO. 1.

2. An isolated polynucleotide comprising a polynucleotide sequence of SEQ ID NO. 1.

3. A recombinant vector sequence comprising SEQ ID NO. 1.

4. An isolated host cell comprising the recombinant vector of claim 3.

5. The isolated host cell of claim 4 which is a cell of E. coli or of Saccharomyces cerevisiae.

6. A method of manufacturing an RNA molecule wherein the recombinant vector of claim 3 is transformed into a bacterial strain, the RNA is transcribed from the vector and the transcribed RNA is isolated and/or purified.

7. An RNA molecule obtained by the method of claim 6.