MAP kinase phosphatase mutant

Details MAP kinase phosphatase mutant MAP kinase phosphatase mutant

2001-01-26

2003-05-20

Monshipouri, M. (Department: 1652)

Organic compounds -- part of the class 532-570 series

Organic compounds

Carbohydrates or derivatives

C435S196000, C435S320100, C435S252300, C435S006120

Reexamination Certificate

active

06566511

ABSTRACT:

The present invention relates to DNA encoding proteins contributing to the regulation of a plant's response to abiotic stress and in particular genotoxic stress.
Cells of all organisms have evolved a series of DNA repair pathways which counteract the deleterious effects of DNA damage and are triggered by intricate signal cascades. To be able to modify or improve DNA repair using gene technology it is necessary to identify key proteins involved in said pathways or cascades. Therefore it is the main object of the present invention to provide DNA comprising an open reading frame encoding such a key protein.
DNA according to the present invention comprises an open reading frame encoding a protein characterized by a stretch of amino acids or component amino acid sequence having 40% or more identity with an aligned component sequence of SEQ ID NO: 3. The protein characterized by SEQ ID NO: 3 is tracked down with the help of a T-DNA tagged Arabidopsis mutant showing hypersensitivity to methyl methanesulfonate (MMS). Said hypersensitivity as well as an observed hypersensitivity to other DNA damaging treatments such as UV light is indicative of the proteins' involvement in the repair of DNA damage, or in signaling pathways implicated in the response to similar genotoxic stress. The mutant is also sensitive to elevated temperature and anti-oxidant N-acetylcysteine. The mutant is not sensitive to osmotic shock, increased salinity, oxidative stress or elevated ehtylene levels. An important characteristic of the mutant is cell death in response to growth in small closed vessels. This phenotype can be complemented by addition of abscisic acid (ABA) to the growth media. Furthermore, the mutant is more sensitive to exogenously applied ABA compared with the wild type which supports the notion that the genes disclosed by the present invention (SEQ ID NO: 1) are involved in stress signaling mediated by ABA.
Sequence alignments of SEQ ID NO: 3 using commercially available computer programs such as BLASTP of the NCBI BLAST family of programs or TFASTA or BestFit of the Wisconsin Package Software, all based on well known algorithms for sequence identity or similarity searches, reveal that stretches of SEQ ID NO: 3 (component sequences) having more than 100 and preferably between 120 to 250 amino acids length can show between 20% and almost 40% sequence identity to aligned stretches of known phosphatases, particularly phosphotyrosine phosphatases, MAP kinase phosphatases or dual specificity phosphatases. Protein phosphatases are classified by their substrate specificities as either phosphoserine/threonine phosphatases (PSTPs) or phosphotyrosine phosphatases (PTPs). The dual specificity phosphatases (DSPs) dephosphorylate both phosphotyrosine and phosphoserine/threonine residues and represent a subfamily of PTPs. MAP kinase phosphatases (MKPs) belong to the family of DSPs. The sequence VHCCQGVSRS (SEQ ID NO: 4) found in SEQ ID NO: 3 can be interpreted as corresponding to the mammalian sequence motif IHCXAGXXRS (SEQ ID NO: 5) defining the family of PTPs, wherein the lie at the first position can be replaced by Val and the Ser at the last position can be replaced by Thr
The present invention defines a new protein family the members of which are characterized by component amino acid sequences of more than 100 amino acid length showing 40% or higher amino acid sequence identity to aligned component sequences of SEQ ID NO: 3. Preferably said component sequences are of more than 120, more than 160 or even more than 200 amino acids length. The amino acid sequence identity is preferably higher than 50% or even higher than 55%. Most preferred are identities higher than 70%.
An example of DNA according to the present invention is described in SEQ ID NO: 1. The amino acid sequence of the protein encoded is identical to SEQ ID NO: 3. After alignment a stretch of the protein having about 140 amino acids shows 36% sequence identity to the MKP-1 protein described by Sun et al (Cell 75: 487-493, 1993). The identity determined after alignment with MKP-2 and MKP-3 is determined as 34% and 26%, respectively. Thus, according to the present invention a protein family related to MAP kinase phosphatases can be defined the members of which after alignment of a stretch of more than 100 amino acids length show 40% or higher amino acid sequence identity to SEQ ID NO: 3. Preferably, the amino acid sequence identity is higher than 50% or even higher than 55%. When making multiple sequence alignments, certain algorithms can take into account sequence similarities, such as same net charge or comparable hydrophobicity/hydrophilicity of the individual amino acids, in addition to sequence identities. The resulting values of sequence similarities, as compared to sequence identities, can help to assign a protein to the correct protein family in border-line cases. Proteins of particular interest, within the scope of the present invention, are MAP kinase phosphatases the amino acid sequence of which comprises at least one of the following characteristic amino acid subsequences:
(a) TSILYDFDYFEDV
(SEQ ID NO: 6)

(b) FVHCCQGVSRST
(SEQ ID NO: 7)

(c) FVHC
(SEQ ID NO: 8)

(d) QGVSRS
(SEQ ID NO: 9)

(e) YFKSD
(SEQ ID NO: 10)
DNA encoding proteins belonging to the new protein family according to the present invention can be isolated from monocotyledonous and dicotyledonous plants. Preferred sources are corn, sugar beet, sunflower, winter oilseed rape, soybean, cotton, wheat, rice, potato, broccoli, cauliflower, cabbage, cucumber, sweet corn, daikon, garden beans, lettuce, melon, pepper, squash, tomato, or watermelon. However, they can also be isolated from mammalian sources such as mouse or human tissues. The following general method, can be used, which the person skilled in the art will normally adapt to his specific task. A single stranded fragment of SEQ ID NO: 1 or SEQ ID NO: 2 consisting of at least 15, preferably 20 to 30 or even more than 100 consecutive nucleotides is used as a probe to screen a DNA library for clones hybridizing to said fragment. The factors to be observed for hybridization are described in Sambrook et al, Molecular cloning: A laboratory manual, Cold Spring Harbor Laboratory Press, chapters 9.47-9.57 and 11.45-11.49, 1989. Hybridizing clones are sequenced and DNA of clones comprising a complete coding region encoding a protein with more than 40% sequence identity to SEQ ID NO: 3 is purified. Said DNA can then be further processed by a number of routine recombinant DNA techniques such as restriction enzyme digestion, ligation, or polymerase chain reaction analysis.
The disclosure of SEQ ID NO: 1 enables a person skilled in the art to design oligonucleotides for polymerase chain reactions which attempt to amplify DNA fragments from templates comprising a sequence of nucleotides characterized by any continuous sequence of 15 and preferably 20 to 30 or more basepairs in SEQ ID NO: 1. Said nucleotides comprise a sequence of nucleotides which represents 15 and preferably 20 to 30 or more basepairs of SEQ ID NO: 1. Polymerase chain reactions performed using at least one such oligonucleotide and their amplification products constitute another embodiment of the present invention.
Knowing the nucleotide sequence of the Arabidopsis MKP1 gene and the amino acid sequence of the encoded protein it is possible to identify proteins interacting with AtMKP1 and to clone their corresponding genes using well known techniques. For example radioactively labeled AtMKP1 protein can be used for interactive cloning on cDNA expression libraries. AtMKP1 protein or parts thereof can be used to generate polyclonal or monoclonal antibodies specific for AtMKP1. The AtMKP1 gene can be used to generate variants of AtMKP1 protein tagged with GST, MYK or His. Said antibodies and MKP1 variants allow to isolate native protein complexes by immunoprecipitation and to determine sequences of proteins present in these complexes by micro-sequencing. The resulting sequence information can in turn be used to clone corresponding genes. Alternatively

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