# Patent

## Title
Plant mitochondria transformation method

## Abstract

Method for heterologous RNA species and protein production in plant cell mitochondria comprising introducing into plant cells nucleic acid components that encode heterologous proteins/RNAS under the control of promoters operative in mitochondria, vectors, host cells, plants and uses thereof.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a National Stage of International Application No. PCT/GB2009/002755 filed Nov. 25, 2009, which claims priority from British Patent Application No. 0821515.4 filed Nov. 25, 2008, the contents of all of which are incorporated herein by reference in their entirety.
The present invention relates to a method for producing heterologous or exogenous RNA species in plant cell material such as genetically transformed plant cells in culture, plant tissue and plants derived from genetically transformed plant cells. In particular, the method relates to a more efficient method for producing RNA species and/or heterologous or exogenous proteins in mitochondria comprised in plant cell material, the genetic material required therefor, such as DNA and RNA, vectors, host cells, methods of introduction of genetic material into plant cells, plant cells comprising genetically modified mitochondria, genetically modified mitochondria and uses thereof.
A disadvantage of prior art plant mitochondrion transformation methods is that the transformation efficiency in terms of numbers of transformed mitochondria per cell tends to be low. Furthermore, the amount of exogenous protein expressed from the mitochondria tends to be low as does the amount of exogenous protein produced per cell. A further disadvantage of prior art methods is that the delivery of genetic information into the mitochondria tends to be erratic in the sense that the delivery mechanisms employed rely on chance for the successful delivery of genetic information, such as RNA, into the mitochondrial genome. Prior art methods do not rely on efficient endogenous cellular processes for the transfer of RNA into the mitochondrial genome, subsequent reverse transcription and recombination of it within the mitochondrial genome, and where appropriate, followed by expression of protein of interest therefrom. As such, prior art processes for genetically modifying the mitochondrion are generally inefficient. These and other disadvantages of prior art mitochondrion transformation technology will become apparent from the foregoing description.
The present inventors have found that by using or adapting endogenous cellular processes for the transfer of polynucleotide sequences, such as RNAs, from the cytoplasm to mitochondria in the plant cell, polynucleotide sequences derived from nuclear transformation of the nucleus of a plant cell can be efficiently transferred or targeted to the mitochondrial genome within a plant cell that is so transformed, and expressed more efficiently in the mitochondrion as described herein. Furthermore, it is apparent that once the mitochondrion is transformed with sequences of the invention, it is not necessary for the nuclear encoded trangenes that are required for the initial transformation of mitochondria to remain in the nuclear genome. As a consequence, the nuclear encoded transgenes can be removed through deliberate or natural segregation in subsequent generations of plants. For the purposes of the present invention the terms “mitochondrion” and “mitochondria” and “mitochondrion population” are used interchangeably, as are the terms “plant cell” and “plant cells”, unless context demands otherwise. By employing or adapting endogenous cellular processes for the transfer of RNA derived from polynucleotide sequences introduced to the nucleus to the mitochondrion genome, as described herein, the method of the invention is considered to be unique over prior art methods for the generation of plant cells or plants possessing genetically modified mitochondria. The mitochondrion population of the plant cell is constantly bombarded by RNA that is derived from the nucleus of the cell, which is carried over the mitochondrial membrane and into the mitochondrial matrix where it is reverse transcribed, integrated into the genome and then transcribed, resulting in the generation of RNA from which proteins of interest may be expressed.
There exists a need for a more efficient mitochondrion transformation method for the production of RNAs, and where required, proteins of interest in the mitochondrion in transformed plant cells and plant tissue derived therefrom. Furthermore, there exists a need for a more efficient nucleic acid based technology, for example an RNA-based technology to knock out genes located within the mitochondria.
The basis for the present invention, which does not appear to have been realised in the prior art, is the supply of a mitochondrial transformation system comprising nucleic acid sequences that encode: i) a plant mitochondria transformation unit (MTU); ii) a reverse transcriptase fused to a plant-derived mitochondrion transit peptide sequence; and iii) an RNA binding protein fused to a plant-derived mitochondrion transit peptide. Such mitochondrial fusion systems do not appear to have been described or alluded to in the prior art. Further simplified modifications of this kind of mitochondrion transformation unit include those that comprise nucleic acid sequences that encode i) a mitochondrion transformation unit (MTU; a mitochondrion translocation sequence (MTS-5′), fused to the 5′ end of the MTU; a further mitochondrion translocation sequence (MTS-3′) fused to the 3′-end of the MTU; and a primer binding domain designed for reverse transcription in the mitochondria using mitochondrion tRNA-Met (PBD-MIT). By placing the PBD-MIT next to the 3′ end of the MTS-3′, that is to say, outside of the LtrB intron as depicted in FIG. 8(A), the LtrA protein is able to function as both a translocation protein and as a source of reverse transcriptase. In such a variant, there is no need to introduce a second gene for reverse transcriptase functionality. In a second variant of this system, where the PBD (PBD-CYT) is designed to interact with endogenous cytoplasmic tRNA-Met, the PBD may be located adjacent to the 3′-end of the MTU and a mitochondrion translocation sequence is fused to it downstream. In this second variant, where a PBD is employed that is able to bind with cytoplasmic tRNA-Met as primer, reverse transcription is initiated by endogenous reverse transcriptase in the cytoplasm using cytoplasmic tRNA-Met. Thus, the second variant of the system does not require the co-delivery of a reverse transcriptase nucleic acid sequence to the mitochondria. The use of such mitochondrial transformation systems provides for an improved yield of RNA or protein of interest (depending on design), from mitochondrial sources than has been hitherto achievable in the prior art.
According to the present invention there is provided a method of transforming a plant cell that comprises:
1) introducing into the said plant cell a first nucleic acid sequence that comprises a plant nuclear promoter operably linked to a first nucleic acid sequence that comprises a plant mitochondrion transgene cassette, a plant mitochondrion translocation sequence, and a primer binding domain;

2) introducing into the said plant cell a second nucleic acid sequence that encodes for a translocation sequence (MTS) binding protein fused to a plant mitochondrion transit peptide wherein said second nucleic acid sequence is operably linked to a plant nuclear promoter; and

3) introducing into the said plant cell a third nucleic acid sequence that encodes for a reverse transcriptase protein fused to a plant mitochondrion transit peptide wherein the third nucleic acid sequence is operably linked to a plant nuclear promoter that drives expression in a plant cell nucleus.

As another aspect of the invention there is provided a plant cell obtained by the method of the invention as described hereinabove and in further refinements of the method as described hereinbelow.
In a further aspect of the invention there is provided a method of transforming a plant cell that comprises introducing into the plant cell a nucleic acid sequence that comprises a plant nuclear promoter operably linked to a first nucleic acid sequence that comprises a first mitochondrion translocation sequence (MTS-5′) fused to the 5′-end of the mitochondrion transformation unit (MTU), a second mitochondrion translocation sequence (MTS-3′) fused to the 3′ end of the MTU, and a primer binding domain designed for reverse transcription in mitochondria, using tRNA-Met located within the mitochondria. The two mitochondrion translocation sequences may be the same or different depending on design. In this variant reverse transcription can be effected when the PBD is located downstream of the MTU, that is to say 3′ to a mitochondrion translocation sequence (MTS-3′). Such a combination allows both translocation of the MTU into the mitochondrion and reverse transcription of the MTU by the LtrA protein and does not require the co-delivery of a nucleic acid sequence for reverse transcriptase functionality.
In a still further variant of the methods aspect of the invention, there is provided a method of transforming a plant cell that comprises introducing into the plant cell a nucleic acid sequence that comprises a plant nuclear promoter operably linked to a first nucleic acid sequence that comprises a first mitochondrion translocation sequence (MTS-5′) fused to the 5′-end of the mitochondrion transgene unit (MTU), a second mitochondrion translocation sequence (MTS-3′) fused to the 3′-end of a primer binding domain for binding tRNA-Met as primer that uses tRNA-Met that is located within the cytoplasm. Thus, the primer binding domain is capable of utilising native, endogenous reverse transcriptase located in the cytoplasm (PBD-CYT) for reverse transcription using cytoplasmic tRNA-Met as primer. Again, the two mitochondrion translocation sequences may be the same or different depending on design. In this variant, there is also no need to co-deliver a nucleic acid sequence to the mitochondria for reverse transcriptase functionality.
As another aspect of the invention there is provided a plant cell obtained by any one of the methods of the invention as described herein above.
In a further aspect of the invention there is provided a method of producing at least a heterologous or exogenous RNA species in a plant that comprises:
1) introducing into a regenerable plant cell a nucleic acid sequence that comprises a plant nuclear promoter operably linked to a first nucleic acid sequence that comprises a plant mitochondrion transgene cassette, a plant mitochondrion translocation sequence, and a primer binding domain;

2) introducing into the said regenerable plant cell a second nucleic acid sequence that encodes for a mitochondrion translocation sequence binding protein fused to a plant mitochondrion transit peptide wherein said second nucleic acid sequence is operably linked to a plant nuclear promoter; and

3) introducing into the said regenerable plant cell a third nucleic acid sequence that encodes for a reverse transcriptase protein fused to a plant mitochondrion transit peptide wherein the third nucleic acid sequence is operably linked to a plant nuclear promoter;

4) growing said regenerable plant cell of steps 1) to 3);

5) selecting a plant cell of (4) wherein the transgene comprised within the plant mitochondrion transgene cassette is integrated into the mitochondrial genome;

6) regenerating a plant from the plant cell of (5); and

7) growing the plant of (6).

Preferably, the plant obtained according to the above method is grown under conditions wherein the said heterologous or exogenous RNA species encoded by the transgene integrated into the mitochondrion is expressed as heterologous or exogenous protein.
Again, and with reference to the method of obtaining a plant above, the skilled addressee will appreciate that where there are native proteins present in a plant cell that are capable of binding to a mitochondrion translocation sequence, and which are capable of translocating RNA nucleic acid sequences to the mitochondrion, such as viroid proteins, step 2) of the said method may be omitted. In such an instance, there is provided a method of producing at least a heterologous or exogenous RNA species in a plant that comprises:
1) introducing into a regenerable plant cell a nucleic acid sequence that comprises a plant nuclear promoter operably linked to a first nucleic acid sequence that comprises a mitochondrion transgene cassette, a mitochondrion translocation sequence (PTS), and a primer binding domain (PBD);

2) introducing into the said regenerable plant cell a second nucleic acid sequence that encodes for a reverse transcriptase protein fused to a second mitochondrion transit peptide wherein the second nucleic acid sequence is operably linked to a plant nuclear promoter that drives expression in a plant cell;

3) growing said regenerable plant cell of steps 1) and 2);

4) selecting a plant cell of (3) wherein the transgene comprised within the mitochondrion transgene cassette is integrated into the plastid genome;

5) regenerating a plant from the plant cell of (4); and

6) growing the plant of (5).

In a further aspect of the invention there is provided a method of producing at least a heterologous or exogenous RNA species in a plant that comprises:
1) introducing into a regenerable plant cell a nucleic acid sequence that comprises a plant nuclear promoter operably linked to a first nucleic acid sequence that comprises a first mitochondrion translocation sequence (MTS-5′) fused to the 5′-end of the mitochondrion transgene or transfromation unit (MTU), a second mitochondrion translocation sequence (MTS-3′) fused to the 3′-end of the MTU, and a primer binding domain for reverse transcription in mitochondria;

2) growing said regenerable plant cell of step 1);

3) selecting a plant cell of (2) wherein the transgene comprised within the mitochondrion transgene cassette is integrated into the mitochondrion genome;

4) regenerating a plant from the plant cell of (3); and

5) growing the plant of (4).

The primer binding domain is designed for reverse transcription in the mitochondria (PBD-MIT), using tRNA-Met as primer that are located within the mitochondria. The two mitochondrion translocation sequences may be the same or different depending on design.
In a further variant of this aspect of the invention there is provided a method of producing at least a heterologous or exogenous RNA species in a plant that comprises:
1) introducing into a regenerable plant cell a nucleic acid sequence that comprises a plant nuclear promoter operably linked to a first nucleic acid sequence that comprises a first mitochondrion translocation sequence (MTS-5′) fused to the 5′-end of the mitochondrion transgene unit (MTU), a second mitochondrion translocation sequence (MTS-3′) fused to the 3′-end of a primer binding domain for binding tRNA-Met as primer that uses tRNA-Met that is located within the cytoplasm.

2) growing said regenerable plant cell of step 1);

3) selecting a plant cell of (2) wherein the transgene comprised within the mitochondrion transgene cassette (MTU) is integrated into the mitochondrion genome;

4) regenerating a plant from the plant cell of (3); and

5) growing the plant of (4).

The primer binding domain in the above variant is capable of utilising native, endogenous reverse transcriptase located in the cytoplasm (PBD-CYT) for reverse transcription using cytoplasmic tRNA-Met as primer. Again, the two mitochondrion translocation sequences may be the same or different depending on design.
Naturally, the person skilled in the art will understand that the plant nuclear promoter by being operably linked to the nucleic acid sequences provided for herein drives expression of such sequences in the plant nucleus.
The “plant mitochondrion transgene cassette” comprises a left flanking sequence (LFS) and a right flanking sequence (RFS) which are used for homologous recombination of the cassette into the mitochondrial genome. In between the LFS and RFS are located at least one mitochondrion specific promoter sequence (mPRO) and at least one mitochondrion specific terminator (mTER) sequence which in turn flanks at least one isolated gene or isolated nucleic acid sequence of interest, such as a recombinant DNA sequence (e.g. cDNA) or an introduced native DNA sequence. The LFS and RFS may include the mPRO and mTER sequences respectively, if for example, the isolated nucleic acid of interest is fused to a native mitochondrial nucleic acid of interest. Thus, the promoter and the terminator sequences are not necessarily included within the LFS or RFS respectively per se, or between the LFS and RFS if a transgene is inserted into the mitochondrial genome as a cistron unit or if a transgene is translationally fused to a native gene.
In such an instance, when a transgene is fused to a native mitochondrial coding sequence it is after the transformation event has taken place that the promoter may be found upstream of the sequence that is homologous to the LFS in the mitochondrial genome and is available to drive expression of the gene fused to the transgene of interest. For the purposes of the present invention “transgene” includes isolated nucleic acid sequences that may ultimately give rise to the expression of proteins or peptides of interest in the mitochondrion as herein described. Thus, the isolated nucleic acid sequence may be one that gives rise to an RNA sequence of interest which may not encode or give rise to the expression of a translatable product, or the isolated nucleic acid sequence may give rise to an RNA sequence that does encode or give rise to the expression of a translatable product such as a protein or peptide of interest. The person skilled in the art will also appreciate that the transgene that is carried on the isolated nucleic acid may also be designed to give rise to an RNA sequence that gives rise to the expression of a translatable product or products, and untranslatable RNAs. Such RNAs that do not give rise to the expression of proteins may give rise to RNA sequences that contain deletions or other mutations and these may find use as research tools for studying gene function in the mitochondrion. Where the “transgene” gives rise to the expression of proteins or peptides, suitable transgenes of interest include plant proteins capable of conferring desired traits to plant crops, and pharmaceutical proteins for use in mammals, including man, such as insulin, preproinsulin, proinsulin, glucagon, interferons such as α-interferon, β-interferon, γ-interferon, blood-clotting factors selected from Factor VII, VIII, IX, X, XI, and XII, fertility hormones including luteinising hormone, follicle stimulating hormone growth factors including epidermal growth factor, platelet-derived growth factor, granulocyte colony stimulating factor and the like, prolactin, oxytocin, thyroid stimulating hormone, adrenocorticotropic hormone, calcitonin, parathyroid hormone, somatostatin, erythropoietin (EPO), enzymes such as β-glucocerebrosidase, haemoglobin, serum albumin, collagen, biotic and abiotic stress proteins, such as insecticidal and insect toxic proteins, for example from, or derived from Bacillus thuringiensis, nematicidal proteins, herbicide resistance proteins, (e.g. to glyphosate), salt-tolerance proteins, drought tolerant proteins, proteins or RNA molecules that are capable of conferring cytoplasmic male sterility to plant breeding lines; nutritional enhancement proteins involved in the biosynthesis of phenolics, starches, sugars, alkaloids, vitamins, and edible vaccines, and the like. Furthermore, the method of the invention can be used for the production of specific monoclonal antibodies or active fragments thereof and of industrial enzymes or active fragments thereof.
All proteins mentioned hereinabove are of the plant and human type. Other proteins that are contemplated for production in the present invention include proteins for use in veterinary care and may correspond to animal homologues of human proteins, such as the human proteins mentioned hereinabove.
In a further aspect of the invention there is provided a plant cell that comprises mitochondria that are permanently transformed with an exogenous or a heterologous nucleic acid sequence that encodes for a protein or RNA of interest. Suitable proteins and peptides and nucleic acids of interest are provided herein. Certain heterologous nucleic acids of interest are useful in conferring cytoplasmic male sterility to plant breeding lines (for example, the petunia mitochondrion pcf sequence (Nivison and Hanson, Plant Cell. 1989 November; 1(11):1121-30.); the ORF79 from BORO-II RICE (Wang et al., 2006; Plant Cell. 2006 March; 18(3):676-87. Epub 2006 Feb. 17.), the orf107 sequence of sorghum (Tang et al., Plant J. 1996 July; 10(1):123-33); the T-urf13 sequence of maize (Dewey et al., EMBO J. 1987 June; 6(6):1541-1546.)
The LFS and RFS may be selected from any nucleotide sequences that may be used for homologous recombination in the mitochondrion. Suitable examples include coding sequences such as the sequence coding for ATP6, ATP9, NAD1, NAD3, from tobacco, Arabidopsis, and rice, (Sugiyama et al., Mol Gen Genomics (2005) 272: 603-615; Unseld et al., (1997) Nat. Genet. 15 (1), 57-61; Notsu et al., Mol. Genet. Genomics 268 (4), 434-445 (2002), ATP1, ATP9 from wheat (Ogihara et al., 2005, Nucleic Acids Res., 33(19): 6235-6250), ATP6, ATP9 from Brassica napus (rapeseed) (Handa, 2003, Nucleic Acids Res. 31 (20), 5907-5916) and non-coding intergenic regions from tobacco, Arabidopsis, rice mitochondria (Sugiyama et al., Mol Gen Genomics (2005) 272: 603-615; Unseld et al., (1997) Nat. Genet. 15 (1), 57-61; Notsu et al., Mol. Genet. Genomics 268 (4), 434-445 (2002).
The mPRO and mTer may be selected from any mitochondrial promoter nucleotide sequences and any mitochondrial terminator nucleotide sequences known in the art. Suitable examples include the ATP6, ATP9, Cob, rrn18, Rps13, Rps19, Cox3, Nad6, Nad9 5′ untranslated sequences (promoter region) of tobacco mitochondria (Sugiyama et al., 2004, Mol Gen Genomics (2005) 272: 603-615) and Arabidopsis mitochondria (Unseld et al., (1997) Nat. Genet. 15 (1), 57-61) and the ATP6, ATP9, Nad6, Nad9 3′ untranslated sequence (terminator region) of tobacco mitochondia (Sugiyama et al., 2004, Mol Gen Genomics (2005) 272: 603-615) and Arabidopsis mitochondria (Unseld et al., (1997) Nat. Genet. 15 (1), 57-61)
The plant mitochondrion transgene cassette also comprises a primer binding domain (PBD) that once inside the mitochondrion is able to capture tRNAs as primers to form template RNA to initiate reverse transcription of introduced plant mitochondrion transformation units of the invention. A suitable tRNA for use in the present invention as a primer is tRNA-fMet which forms a template RNA ready for reverse transcription. The skilled person in the art will appreciate that PBDs are found naturally on retroelements including retroviruses and retrotransposons. PBDs comprise specific RNA domains that anneal to specific sequences on tRNA molecules. The tRNA itself does not serve as a PBD but as a primer for reverse transcription, the template for reverse transcription is the RNA molecule that carries a PBD. Novel PBDs can be readily engineered that can anneal to other tRNAs, for example any of the known 23 mitochondrial tRNAs. The tRNA itself is not the template but is used as a primer that binds to PBD on the MTU RNA template (FIG. 1).
PBDs can be designed to bind other types of tRNAs such as, tRNA-lys and tRNA-Met of tobacco mitochondria (and identified tRNAs of tobacco (23) Genbank, NC 006581), Arabidopsis mitochondria, and rice mitochondria (Notsu et al., Mol. Genet. Genomics 268 (4), 434-445 (2002).
Certain elements of retroelements such as retroviruses or retrotransposons, have native PBDs possessing conserved domains that anneal with complementary domains from tRNA (usually tRNA-met, or tRNA-trp); because of the conserved structures of all tRNAs (the so-called clover-leaf structure), PBDs can be engineered so that they carry specific domains that will anneal with a tRNA of choice.
A “plant mitochondrion translocation sequence” (MTS) is an RNA sequence that is capable of being bound to a plant MTS binding protein and thereby, the MTS and other RNA sequences that may be associated with it or fused with it can be transported across and into the mitochondrion. The MTS can be selected from naked RNA viruses, including the mitoviruses of the Narnaviridae, such as from Cryphonectria mitovirus 1 (CMV1),
Ophiostoma mitovirus 3a (OMV3a), Sclerotinia homoeocarpa mitovirus, Ophiostoma mitovirus 4 (OMV4), Ophiostoma mitovirus 5 (OMV5),
Ophiostoma mitovirus 6 (OMV6), Botrytis cinerea debilitation-related virus, Cryphonectria cubensis mitovirus 1a, Cryphonectria cubensis mitovirus 1b, Cryphonectria cubensis mitovirus 1c, Cryphonectria cubensis mitovirus 2a, Cryphonectria cubensis mitovirus 2b, Cryphonectria cubensis mitovirus 2c, Gremmeniella mitovirus S1 (GMVS1), Gremmeniella mitovirus S2, Helicobasidium mompa mitovirus 1-18, Ophiostoma mitovirus 1a (OMV1a),

Ophiostoma mitovirus 1b (OMV1b), Ophiostoma mitovirus 2 (OMV2), Ophiostoma mitovirus 3b (OMV3b), Thielaviopsis basicola mitovirus, Cryphonectria mitovirus I, viral RNAs such as those from positive stranded RNA viruses such as potato virus X (PVX), tobacco mosaic virus (TMV), tomato mosaic virus (ToMV), and viral RNAs from negative stranded RNA viruses, such as tomato spotted wilt virus (TSWV) and Impatiens necrotic spotted virus (INSV), viroids such as potato spindle tuber viroid PSTVd), satellite viruses such as satellite tobacco mosaic virus (STMV) and the like. Other sources of the MTS include group I and group II intron RNAs or modified versions thereof in which cryptic splicing sites have been eliminated that may be derived from a bacterium, a fungus or a mitochondrion from a plant, such as an LTRB intron lacking the sequence coding for LTRA (the protein encoded by an LTRA sequence being capable of serving as an MTS-binding protein in the methods of the invention).

Preferably, the intron is a group II intron, such as the Lactococcus lactis Ll.ltrB intron or a modified version of it in which cryptic splicing sites have been eliminated as outlined herein. Group II introns are widely represented in the organelles of plants and fungi, and in bacteria. Group II introns useful in the method of the invention are mobile, highly structural retroelements that encode multifunctional protein (intron encoded protein or IEP) which possesses reverse transcriptase (RT) activity. The IEP facilitates splicing of intron RNA by stabilization of the catalytically active RNA structure, performs reverse transcription and insertion of the intron into specific DNA target sites of the bacterial genome at high frequency (Moran et al. (1995) Mol Cell Biol 15:2828-2838; Cousineau et al. (1998) Cell 94:451-462).
Group II introns of bacterial origin, such as those derived from Lactococcus that comprise a modified LtrA gene, are preferably used in the method of the invention. The LtrA polynucleotide sequence of a Lactococcus bacterium, such as Lactococcus lactis may be modified for optimum expression in plants by inserting into it at least one polynucleotide sequence comprising one or more introns from at least one plant nucleic acid sequence, such as from one or more plant genes and by substituting certain selected codons having a low frequency of usage in native plants with codons that occur with a higher frequency in such plants. Typically, the bacterial LtrA sequence of interest is analysed with reference to plant codon usage using in silico comparisons such as those found at the website www.kazusa.or.jp/codon for bacterial codons that occur with low frequency in plants. Such codons may then be substituted with codons that have a high frequency of occurrence in plants, and an in silico-derived modified polynucleotide sequence is generated. From this optimised LtrA sequence a synthetic LtrA polynucleotide sequence corresponding to the in silico generated sequence is made using standard polynucleotide synthesis procedures known in the art, and may then be used in the preparation of constructs of use in the present invention as outlined herein. It is thought that by using a modified sequence that comprises plant codon substitutions as outlined above more plant cell environment stable polynucleotide RNA sequences are generated.
Other types of introns that may be used in the method of the invention include, for example, the group I intron from Tetrahymena (GenBank Acc. No.: X54512; Kruger K et al. (1982) Cell 31:147-157; Roman J and Woodson S A (1998) Proc Natl Acad Sci USA 95:2134-2139), the group II rIl intron from Scenedesmus obliquus (GenBank Acc. No.: X17375.2 nucleotides 28831 to 29438; Hollander V and Kuck U (1999) Nucl Acids Res 27: 2339-2344; Herdenberger F et al. (1994) Nucl Acids Res 22: 2869-2875; Kuck V et al. (1990) Nucl Acids Res 18:2691-2697), and the Ll.LtrB intron (GenBank Acc. No.: U50902 nucleotides 2854 to 5345).
Aside from heterologous introns described herein, endogenous introns that occur naturally in the mitochondria, such as group II introns from plant mitochondria, for example the NAD4 intron 1 from Arabidopsis (Unseld et al., (1997) Nat. Genet. 15 (1), 57-61), the NAD4 intron 1 from tobacco_(Sugiyama et al., Mol Gen Genomics (2005) 272: 603-615) or from maize Clifton et al., Plant Physiol. 136 (3), 3486-3503 (2004)), or from wheat (Ogigara et al., Nucleic Acids Res. 33 (19), 6235-6250 (2005)) or the Cox II intron and NADII intron 2 from wheat (Nucleic Acids Res. 33 (19), 6235-6250 (2005). Introns which occur naturally in the mitochondria of the plant of interest may be modified such that they have a sequence homology of about 50%, 60%, 70%, 75%, 80%, 85%, 90% or 95%, or of any percentage sequence homology therebetween, with the sequence of the starting intron, while retaining functionality, may also be employed in the method of the invention. Other MTS include RNA domains found on tobacco TNT1, yeast Ty1- and Ty3-like retrotransposons or other RNA that harbours a domain that is recognised by an RNA binding protein that is driven into the mitochondria.
A “mitochondrion translocation sequence binding protein” (MTS-BP) can be any RNA binding protein that recognises and binds to specific RNA domains of interest and is fused to a mitochondrial transit peptide. Examples of suitable MTS-BP proteins may be selected from
the Ltra protein from the group II intron II Ltrb, coat proteins that bind to RNA viruses such as the coat protein from potato virus X (PVX), the coat protein of TMV, RNA-dependent RNA polymerases (RdRpS) of RNA viruses such as the replicases of PVX or TMV, reverse transcriptase protein from retrotransposons, such as tobacco TnT1, yeast Tyl-1 which recognise structures on the retrotransposon RNA molecule, and proteins that bind to cellular RNAs such as translation elongation factor proteins and ribosomal binding proteins. Preferably, MTS-BP protein is the LrtA protein from the group II intron 11Ltrb.
A “plant mitochondrion transit peptide” (TP) is one that may be derived or obtained from a mitochondrion-targeted protein, for example those described by Boutry et al Nature 328340-342 (1987), the signal peptide from the tobacco F1-ATPase β subunit and the Arabidopsis CPN60 protein and those that may be predicted by Mitochondrial localisation programmes such as “Predotar” and SignalP(Predotar: a neural network-based prediction service for identifying putative mitochondrial and ER targeting sequences urgi.versailles.inra.fr/predotar/predotar.html; SIGNALP (www.cbs.dtu.dk/services/SignalP).
The “mitochondrion reverse transcriptase” protein, if employed, may be selected from a retrovirus source, such as from plant retroviruses such as SIRE-1 from soybean, or from a retrotransposon source such as from the yeast Tyl1 retrotransposon, for example the reverse transcriptase-RNaseH domain (Goffeau et al., Science 274 (5287), 546-547 (1996)) or the tobacco TnT1 retrotrasnposon (RTRH domain) (Vernhettes et., al.; Mol. Biol. Evol. 15 (7), 827-836 (1998)).
A plant nuclear promoter (for example, an exogenous nucleus specific promoter) is one that is able to drive expression of a nucleic acid sequence such as a cDNA sequence or a full length gene sequence in the nucleus of a plant cell, forming a transcribed RNA sequence. The plant nuclear promoter is one that is introduced in front of a nucleic acid sequence of interest and is operably associated therewith. Thus a plant nuclear promoter is one that has been placed in front of a selected polynucleotide component. Typically, a plant nuclear promoter, such as an exogenous nucleus specific promoter, is one that is transferred to a host cell or host plant from a source other than the host cell or host plant.
The cDNAs encoding a polynucleotide of the invention contain at least one type of nucleus specific promoter that is operable in a plant cell, for example, an inducible or a constitutive promoter operatively linked to a first and/or second nucleic acid sequence or nucleic acid sequence component as herein defined and as provided by the present invention. As discussed, this enables control of expression of polynucleotides of the invention. The invention also provides plants transformed with polynucleotide sequences or constructs and methods including introduction of such polynucleotide nucleic acid sequences or constructs into a plant cell and/or induction of expression of said first or second nucleic acid sequence or construct within a plant cell, e.g. by application of a suitable stimulus, such as an effective exogenous inducer.
The term “inducible” as applied to a promoter is well understood by those skilled in the art. In essence, expression under the control of an inducible promoter is “switched on” or increased in response to an applied stimulus (which may be generated within a cell or provided exogenously). The nature of the stimulus varies between promoters. Some inducible promoters cause little or undetectable levels of expression (or no expression) in the absence of the appropriate stimulus. Other inducible promoters cause detectable constitutive expression in the absence of the stimulus. Whatever the level of expression is in the absence of the stimulus, expression from any inducible promoter is increased in the presence of the correct stimulus. The preferable situation is where the level of expression increases upon application of the relevant stimulus by an amount effective to alter a phenotypic characteristic. Thus an inducible (or “switchable”) promoter may be used which causes a basic level of expression in the absence of the stimulus which level is too low to bring about a desired phenotype (and may in fact be zero). Upon application of the stimulus, expression is increased (or switched on) to a level, which brings about the desired phenotype. One example of an inducible promoter is the ethanol inducible gene switch disclosed in Caddick et al (1998) Nature Biotechnology 16: 177-180. A number of inducible promoters are known in the art.
Chemically regulated promoters can be used to modulate the expression of a gene or a polynucleotide sequence of the invention in a plant through the application of an exogenous chemical regulator. Depending upon the objective, the promoter may be a chemically inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression. Chemically inducible promoters are known in the art and include, but are not limited to, the maize In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR-1a promoter, which is activated by salicylic acid. Other chemically regulated promoters of interest include steroid-responsive promoters (see, for example, the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis et al. (1998) Plant J. 14(2):247-257) and tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet. 227:229-237, and U.S. Pat. Nos. 5,814,618 and 5,789,156), herein incorporated by reference.
Where enhanced expression in particular tissues is desired, tissue-specific promoters can be utilized. Tissue-specific promoters include those described by Yamamoto et al. (1997) Plant J. 12(2)255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen. Genet. 254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2):157-168; Rinehart et al. (1996) Plant Physiol. 112(3):1331-1341; Van Camp et al. (1996) Plant Physiol. 112(2):525-535; Canevascini et-al. (1996) Plant Physiol. 112(2):513-524; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Lam (1994) Results Probl. Cell Differ. 20:181-196; Orozco et al. (1993) Plant Mol. Biol. 23(6):1129-1138; Matsuoka et al. (1993) Proc Natl. Acad. Sci. USA 90(20):9586-9590; and Guevara-Garcia et al. (1993) Plant J. 4(3):495-505.
So-called constitutive promoters may also be used in the methods of the present invention. Constitutive promoters include, for example, CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet. 81:581-588); MAS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. application Ser. No. 08/409,297), and the like. Other constitutive promoters include those in U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; and 5,608,142. In a preferment, the plant nuclear promoter used in the method of the invention is a constitutive promoter.
The expression in the mitochondrion is effected by employing a plant mitochondrion promoter such as mitochondrion specific promoters and/or transcription regulation elements. Examples include the ATP6 promoter from tobacco or Arabidopsis mitochondria, the ATP9 promoter from Arabidopsis or tobacco mitochondria or the mitochondrion specific promoter may have a polycistronic “operon” assigned to it, such as the Orf125-NAD3-RSP12 region from tobacco (Sugiyama et al., Mol Gen Genomics (2005) 272: 603-615) or the NAD3-RPS12-Orf299-orf156 region from wheat mitochondria (Clifton et al., Plant Physiol. 136 (3), 3486-3503 (2004).
In another aspect of the invention there is provided a mitochondrion transformation sequence that comprises:
i) a plant mitochondrion translocation sequence;
ii) a mitochondrion transgene cassette; and
iii) a primer binding domain.
The plant mitochondrion translocation sequence and the primer binding domain are as defined herein.
The mitochondrion transgene cassette comprises a left flanking sequence (LFS) and a right flanking sequence (RFS) as herein described, and may include a promoter region and/or a terminator region sourced from a higher or lower plant mitochondrion, for example from tobacco, arabidopsis, brassica sp., potato, corn (maize), canola, rice, wheat, barley, brassica sp., cotton, algae (e.g. blue green species), lemnospora (“duckweed”), or moss (e.g. physcomitrella patens). Preferably, the mPRO and mTER regions are sourced from higher plant species. Where the LFS and RFS do not include a promoter and/or a terminator region, these components may be placed adjacent to the LFS and/or RFS, as appropriate, or there may be a spacer region therein between. Included within the mitochondrion transgene cassette is at least one transgene or one nucleotide sequence of choice that is destined to be transcribed and/or translated in the mitochondrion in accordance with the design of the method of the present invention for example, for the production of desired protein(s), RNAs of interest, or knockout of endogenous mitochondrial genes and regulatory sequences. Suitable transgenes of interest contemplated for protein or peptide production in a method of the present invention include plant proteins and pharmaceutical proteins for use in mammals, including man, such as insulin, preproinsulin, proinsulin, glucagon, interferons such as α-interferon, β-interferon, γ-interferon, blood-clotting factors selected from Factor VII, VIII, IX, X, XI, and XII, fertility hormones including luteinising hormone, follicle stimulating hormone growth factors including epidermal growth factor, platelet-derived growth factor, granulocyte colony stimulating factor and the like, prolactin, oxytocin, thyroid stimulating hormone, adrenocorticotropic hormone, calcitonin, parathyroid hormone, somatostatin, erythropoietin (EPO), enzymes such as β-glucocerebrosidase, haemoglobin, serum albumin, collagen, insect toxic protein from Bacillus thuringiensis; herbicide resistance protein (glyphosate); salt-tolerance proteins; proteins involved in conferring cytoplasmic male sterility to plant breeding lines; nutritional enhancement proteins involved in the biosynthesis of phenolics, starches, sugars, alkaloids, vitamins, and edible vaccines, and the like. Furthermore, the method of the invention can be used for the production of specific monoclonal antibodies, or active fragments thereof and of industrial enzymes.
All proteins mentioned hereinabove are of the plant and human type. Other proteins that are contemplated for production in the present invention include proteins for use in veterinary care and may correspond to animal homologues of human proteins, such as the human proteins mentioned hereinabove.
In a further aspect of the invention there is provided a plant cell that comprises mitochondria that are permanently transformed with an exogenous or a heterologous nucleic acid sequence that encodes for a protein of interest. Suitable proteins and peptides of interest may be selected from those provided herein. Certain heterologous nucleic acids of interest are useful in conferring cytoplasmic male sterility to plant breeding lines such as the petunia mitochondrion pcf sequence (Nivison and Hanson, Plant Cell. 1989 November; 1(11):1121-30.); the ORF79 from BORO-II RICE (Wang et al., 2006; Plant Cell. 2006 March; 18(3):676-87. Epub 2006 Feb. 17.), the orf107 sequence of sorghum (Tang et al., Plant J. 1996 July; 10(1):123-33); the T-urf13 sequence of maize (Dewey et al., EMBO J. 1987 June; 6(6):1541-1546) and as a consequence plant breeding lines breeding true for male sterility may be achieved in far fewer generations of crosses, for example in one generation or two generations. The invention provides for the first time, a reliable means by which to confer permanent cytoplasmic male sterility in male plant breeding lines without the need for engaging in multiple crossings over generations of plants, thus speeding up breeding processes where male sterile lines are desired, for example in brassica species such as in cauliflower, broccoli (e.g. green and purple sprouting), cabbage (e.g. red, green and white cabbages), curly kale, Brussels sprouts, tomato, capsicum, squashes, canola (rape), sunflower, soyabean, corn (maize), rice, wheat, barley and the like. In a preferment of this aspect of the invention, there is provided a plant cell comprising mitochondria that are permanently transformed with an exogenous or a heterologous nucleic acid sequence that encodes for a protein that is capable of conferring cytoplasmic male sterility to a plant derived from the said plant cell. Accordingly, there is also provided a plant derived from a plant cell as described herein.
Naturally, the person skilled in the art will appreciate that where nuclear terminator DNA sequences will be present in constructs used in the invention, these are contemplated as comprising a DNA sequence at the end of a transcriptional unit which signals termination of transcription. These elements are 3′-non-translated sequences containing polyadenylation signals, which act to cause the addition of polyadenylate sequences to the 3′ end of primary transcripts. For expression in plant cells the nopaline synthase transcriptional terminator (A. Depicker et al., 1982, J. of Mol. & Applied Gen. 1:561-573) sequence serves as a transcriptional termination signal.
Those skilled in the art are well able to construct vectors and design protocols for recombinant nucleic acid sequences or gene expression. Suitable vectors can be chosen or constructed, containing appropriate regulatory sequences, including promoter sequences, terminator fragments, polyadenylation sequences, enhancer sequences, marker genes and other sequences as appropriate. For further details see, for example, Molecular Cloning: a Laboratory Manual: 2nd edition, Sambrook et al, 1989, Cold Spring Harbor Laboratory Press. Many known techniques and protocols for manipulation of nucleic acid, for example in preparation of nucleic acid constructs, mutagenesis, sequencing, introduction of DNA into cells and gene expression, and analysis of proteins, are described in detail in Current Protocols in Molecular Biology, Second Edition, Ausubel et al. eds., John Wiley & Sons, 1992. The disclosures of Sambrook et al. and Ausubel et al. are incorporated herein by reference. Specific procedures and vectors previously used with wide success upon plants are described by Bevan (Nucl. Acids Res. 12, 8711-8721 (1984)) and Guerineau and Mullineaux (1993) (Plant transformation and expression vectors. In: Plant Molecular Biology Labfax (Croy RRD ed.) Oxford, BIOS Scientific Publishers, pp 121-148).
Naturally, the skilled addressee will appreciate that each introduced transgene in a transgene cassette will be under regulatory control of its own exogenous mitochondrial promoter and mitochondrial terminator. When two or more target proteins are destined to be produced from a single carrier RNA it is preferable if they are able to be readily separated, for example by binding to different protein-specific antibodies (monoclonal or polyclonal) in the harvesting phase of the plant cell culture system.
Selectable genetic markers may facilitate the selection of transgenic plants and these may consist of chimaeric genes that confer selectable phenotypes such as resistance to antibiotics such as spectinomycin, streptomycin, kanamycin, neomycin, hygromycin, puramycin, phosphinotricin, chlorsulfuron, methotrexate, gentamycin, spectinomycin, imidazolinones and glyphosate.
When introducing selected nucleic acid sequences according to the present invention into a cell, certain considerations must be taken into account, well known to those skilled in the art. The nucleic acid to be inserted should be assembled within a construct, which contains effective regulatory elements, which will drive transcription. There must be available a method of transporting the construct into the cell. Once the construct is within the cell, integration into the endogenous chromosomal material either will or will not occur. Finally, as far as plants are concerned the target cell type must be such that cells can be regenerated into whole plants.
Plants transformed with DNA segments containing sequences of interest as provided herein may be produced by standard techniques, which are already known for the genetic manipulation of plants. DNA can be transformed into plant cells using any suitable technology, such as a disarmed Ti-plasmid vector carried by Agrobacterium exploiting its natural gene transfer ability (EP-A-270355, EP-A-0116718, NAR 12(22) 8711-87215 1984), particle or micro projectile bombardment (U.S. Pat. No. 5,100,792, EP-A-444882, EP-A-434616) microinjection (WO 92/09696, WO 94/00583, EP 331083, EP 175966, Green et al. (1987) Plant Tissue and Cell Culture, Academic Press), electroporation (EP 290395, WO 8706614) other forms of direct DNA uptake (DE 4005152, WO 9012096, U.S. Pat. No. 4,684,611), liposome mediated DNA uptake (e.g. Freeman et al. Plant Cell Physiol. 29: 1353 (1984)), or the vortexing method (e.g. Kindle, PNAS U.S.A. 87: 1228 (1990d) Physical methods for the transformation of plant cells are reviewed in Oard, 1991, Biotech. Adv. 9: 1-11.
Thus once a nucleic acid sequence or gene has been identified, it may be reintroduced into plant cells using techniques well known to those skilled in the art to produce transgenic plants of the appropriate phenotype.
Agrobacterium transformation is widely used by those skilled in the art to transform dicotyledonous species. Production of stable, fertile transgenic plants in almost all economically relevant monocot plants is also now routine: (Toriyama, et al. (1988) Bio/Technology 6, 1072-1074; Zhang, et al. (1988) Plant Cell Rep. 7, 379-384; Zhang, et al. (1988) Theor. Appl. Genet. 76, 835-840; Shimamoto, et al. (1989) Nature 338, 274-276; Datta, et al. (1990) Bio/Technology 8, 736-740; Christou, et al. (1991) Bio/Technology 9, 957-962; Peng, et al. (1991) International Rice Research Institute, Manila, Philippines 563-574; Cao, et al. (1992) Plant Cell Rep. 11, 585-591; Li, et al. (1993) Plant Cell Rep. 12, 250-255; Rathore, et al. (1993) Plant Molecular Biology 21, 871-884; Fromm, et al. (1990) Bio/Technology 8, 833-839; Gordon-Kamm, et al. (1990) Plant Cell 2, 603-618; D'Halluin, et al. (1992) Plant Cell 4, 1495-1505; Walters, et al. (1992) Plant Molecular Biology 18, 189-200; Koziel, et al. (1993) Biotechnology 11, 194-200; Vasil, I. K. (1994) Plant Molecular Biology 25, 925-937; Weeks, et al. (1993) Plant Physiology 102, 1077-1084; Somers, et al. (1992) Bio/Technology 10, 1589-1594; WO92/14828). In particular, Agrobacterium mediated transformation is now a highly efficient alternative transformation method in monocots (Hiei et al. (1994) The Plant Journal 6, 271-282).
The generation of fertile transgenic plants has been achieved in the cereals rice, maize, wheat, oat, and barley (reviewed in Shimamoto, K. (1994) Current Opinion in Biotechnology 5, 158-162.; Vasil, et al. (1992) Bio/Technology 10, 667-674; Vain et al., 1995, Biotechnology Advances 13 (4): 653-671; Vasil, 1996, Nature Biotechnology 14 page 702). Wan and Lemaux (1994) Plant Physiol. 104: 37-48 describe techniques for generation of large numbers of independently transformed fertile barley plants.
Micro projectile bombardment, electroporation and direct DNA uptake are preferred where Agrobacterium is inefficient or ineffective. Alternatively, a combination of different techniques may be employed to enhance the efficiency of the transformation process, e.g. bombardment with Agrobacterium coated micro particles (EP-A-486234) or micro projectile bombardment to induce wounding followed by co-cultivation with Agrobacterium (EP-A-486233).
Following transformation, a plant may be regenerated, e.g. from single cells, callus tissue or leaf discs, as is standard in the art. Almost any plant can be entirely regenerated from cells, tissues and organs of the plant. Available techniques are reviewed in Vasil et al., Cell Culture and Somatic Cell Genetics of Plants, Vol. I, II and III, Laboratory Procedures and Their Applications, Academic Press, 1984, and Weiss Bach and Weiss Bach, Methods for Plant Molecular Biology, Academic Press, 1989.
The particular choice of a transformation technology will be determined by its efficiency to transform certain plant species as well as the experience and preference of the person practising the invention with a particular methodology of choice. It will be apparent to the skilled person that the particular choice of a transformation system to introduce nucleic acid into plant cells is not essential to or a limitation of the invention, nor is the choice of technique for plant regeneration.
The invention further encompasses a host cell transformed with vectors or constructs as set forth above, especially a plant or a microbial cell. Thus, a host cell, such as a plant cell, including nucleotide sequences of the invention as herein indicated is provided. Within the cell, the nucleotide sequence may be incorporated within the chromosome.
Also according to the invention there is provided a plant cell having incorporated into its genome at least a nucleotide sequence, particularly heterologous nucleotide sequences, as provided by the present invention under operative control of regulatory sequences for control of expression as herein described. The coding sequence may be operably linked to one or more regulatory sequences which may be heterologous or foreign to the nucleic acid sequences employed in the invention, such as those not naturally associated with the nucleic acid sequence(s) for its (their) expression. The nucleotide sequence according to the invention may be placed under the control of an externally inducible promoter to place expression under the control of the user. A further aspect of the present invention provides a method of making such a plant cell involving introduction of nucleic acid sequence(s) contemplated for use in the invention or a suitable vector including the sequence(s) contemplated for use in the invention into a plant cell and causing or allowing recombination between the vector and the plant cell genome to introduce the said sequences into the genome. The invention extends to plant cells containing a nucleotide sequence according to the invention as a result of introduction of the nucleotide sequence into an ancestor cell.
The term “heterologous” may be used to indicate that the gene/sequence of nucleotides in question have been introduced into said cells of the plant or an ancestor thereof, using genetic engineering, i.e. by human intervention. A transgenic plant cell, i.e. transgenic for the nucleotide sequence in question, may be provided. The transgene may be on an extra-genomic vector or incorporated, preferably stably, into the genome. A heterologous gene may replace an endogenous equivalent gene, i.e. one that normally performs the same or a similar function, or the inserted sequence may be additional to the endogenous gene or other sequence. An advantage of introduction of a heterologous gene is the ability to place expression of a sequence under the control of a promoter of choice, in order to be able to influence expression according to preference. Furthermore, mutants, variants and derivatives of the wild-type gene, e.g. with higher activity than wild type, may be used in place of the endogenous gene. Nucleotide sequences heterologous, or exogenous or foreign, to a plant cell may be non-naturally occurring in cells of that type, variety or species. Thus, a nucleotide sequence may include a coding sequence of or derived from a particular type of plant cell or species or variety of plant, placed within the context of a plant cell of a different type or species or variety of plant. A further possibility is for a nucleotide sequence to be placed within a cell in which it or a homologue is found naturally, but wherein the nucleotide sequence is linked and/or adjacent to nucleic acid which does not occur naturally within the cell, or cells of that type or species or variety of plant, such as operably linked to one or more regulatory sequences, such as a promoter sequence, for control of expression. A sequence within a plant or other host cell may be identifiably heterologous, exogenous or foreign.
Plants which include a plant cell according to the invention are also provided, along with any part or propagule thereof, seed, selfed or hybrid progeny and descendants. Particularly provided are transgenic crop plants, which have been engineered to carry genes identified as stated above. Examples of suitable plants include tobacco (Nicotiana tabacum) and other Nicotiana species, carrot, vegetable and oilseed Brassicas, melons, Capsicums, grape vines, lettuce, strawberry, sugar beet, wheat, barley, corn (maize), rice, soybean, peas, sorghum, sunflower, tomato, cotton, and potato. Especially preferred transgenic plants of the invention include cotton, rice, oilseed Brassica species such as canola, corn (maize) and soybean.
In addition to a plant, the present invention provides any clone of such a plant, seed, selfed or hybrid progeny and descendants, and any part of any of these, such as cuttings, seed. The invention provides any plant propagule that is any part which may be used in reproduction or propagation, sexual or asexual, including cuttings, seed and so on. Also encompassed by the invention is a plant which is a sexually or asexually propagated offspring, clone or descendant of such a plant, or any part or propagule of said plant, offspring, clone or descendant.
The present invention also encompasses the polypeptide expression product of a nucleic acid molecule according to the invention as disclosed herein or obtainable in accordance with the information and suggestions herein. Also provided are methods of making such an expression product by expression from a nucleotide sequence encoding therefore under suitable conditions in suitable host cells e.g. E. coli. Those skilled in the art are well able to construct vectors and design protocols and systems for expression and recovery of products of recombinant gene expression.
The heterologous or exogenous target protein is contemplated to be any protein of interest that may be produced by the method of the invention.
A polypeptide according to the present invention may be an allele, variant, fragment, derivative, mutant or homologue of the (a) polypeptides as mentioned herein. The allele, variant, fragment, derivative, mutant or homologue may have substantially the same function of the polypeptides alluded to above and as shown herein or may be a functional mutant thereof.
“Homology” in relation to an amino acid sequence or polypeptide sequence produced by the method of the invention may be used to refer to identity or similarity, preferably identity. As noted already above, high level of amino acid identity may be limited to functionally significant domains or regions.
In certain embodiments, an allele, variant, derivative, mutant derivative, mutant or homologue of the specific sequence may show little overall homology, say about 20%, or about 25%, or about 30%, or about 35%, or about 40% or about 45%, with the specific sequence. However, in functionally significant domains or regions, the amino acid homology may be much higher. Putative functionally significant domains or regions can be identified using processes of bioinformatics, including comparison of the sequences of homologues.
Functionally significant domains or regions of different polypeptides may be combined for expression from encoding nucleic acid as a fusion protein. For example, particularly advantageous or desirable properties of different homologues may be combined in a hybrid protein, such that the resultant expression product, may include fragments of various parent proteins, if appropriate.
Similarity of amino acid sequences may be as defined and determined by the TBLASTN program, of Altschul et al. (1990) J. Mol. Biol. 215: 403-10, which is in standard use in the art. In particular, TBLASTN 2.0 may be used with Matrix BLOSUM62 and GAP penalties: existence: 11, extension: 1. Another standard program that may be used is BestFit, which is part of the Wisconsin Package, Version 8, September 1994, (Genetics Computer Group, 575 Science Drive, Madison, Wis., USA, Wisconsin 53711). BestFit makes an optimal alignment of the best segment of similarity between two sequences. Optimal alignments are found by inserting gaps to maximize the number of matches using the local homology algorithm of Smith and Waterman (Adv. Appl. Math. (1981) 2: 482-489). Other algorithms include GAP, which uses the Needleman and Wunsch algorithm to align two complete sequences that maximizes the number of matches and minimizes the number of gaps. As with any algorithm, generally the default parameters are used, which for GAP are a gap creation penalty=12 and gap extension penalty=4. Alternatively, a gap creation penalty of 3 and gap extension penalty of 0.1 may be used. The algorithm FASTA (which uses the method of Pearson and Lipman (1988) PNAS USA 85: 2444-2448) is a further alternative.
Use of either of the terms “homology” and “homologous” herein does not imply any necessary evolutionary relationship between compared sequences, in keeping for example with standard use of terms such as “homologous recombination” which merely requires that two nucleotide sequences are sufficiently similar to recombine under the appropriate conditions. Further discussion of polypeptides according to the present invention, which may be encoded by nucleic acid according to the present invention, is found below.
The teaching of all references cited herein is incorporated in its entirety into the present description.



There now follow non-limiting examples and figures illustrating the invention.
FIG. 1: Major components of the plant mitochondria transformation system.
(1) Mitochondria transformation unit (MTU) (i) a plant mitochondrion translocation sequence (MTS); (ii) a mitochondrion transgene cassette comprising: a left flanking sequence (LFS)1 and right flanking sequence (RFS)1 to facilitate insertion of the cassette into the mitochondria genome using homologous recombination, a promoter region from tobacco mitochondria (mPro)1, a sequence (transgene) of interest (TG), a transcription terminator from the tobacco mitochondrial genome (mTER)1; and (iii) a primer binding domain (PBD). (2) Reverse Transcriptase-RNase H gene translationally fused to the mitochondria transit peptide from tobacco F1-ATPAse beta subunit (mTP). (3) MTS-Binding peptide translationally fused to the mitochondria transit peptide from Tobacco F1-ATPAse beta subunit (mTP).1 mPRO and mTER can be part of LFS and RFS respectively, if for example the transgene is fused to a native mitochondrial gene.
FIG. 2: Schematic representation of the mitochondria transformation system
(1) Targeting of RNA-protein complexes to the plant mitochondria.
(a) After transformation of the mitochondria transformation unit (MTU) construct into the plant genome a strong expression of the MTU RNA which contains the mitochondria targeting cassette and mitochondria translocation sequence (MTS) is achieved from a nuclear specific promoter. The MTS-binding protein (MTS-BP) is expressed from a separate cassette. (b) Both MTS-BP and MTU RNAs are transferred from the nucleus into the cytoplasm where MTS-BP is translated. and (c) binds to the MTU RNA via recognition of MTS to form the MTU/MTS-BP nucleoprotein complex. (d) As MTS-BP carries a mitochondria transit peptide it preferentially transfers the MTU/MTS-BP complex into the mitochondria. Once MTU is presented in the plant cell via nuclear transformation, the mitochondria will then be permanently bombarded by the expressed MTU/MTS-BP complex. Such stable and continuous pumping of the complex into the targeted organelle is a prerequisite for achieving a high efficiency of organelle transformation.
(2) Reverse transcription and insertion into the mitochondrial genome.
The third component of the mitochondria transformation system is the mitochondria-targeted reverse transcriptase-RNaseH protein (MRT-RH). (e) MRT-RH is expressed from a nuclear expression cassette and (f) is driven to the mitochondria by its mitochondria transit peptide. (g) Once inside the organelle, MRT-RH catalyses reverse transcription of the MTU RNA primed with tRNA-Met. (h) Insertion of the reverse transcribed cassette into the mitochondrial genome is induced due to homologous recombination between sequences flanking the mitochondria transgene cassette and the homologous sequences in the mitochondrial genome.
FIG. 3: M21 and M28 constructs
M21 Construct
The binary vector pGreen0029 was used as a backbone and enables selection of transgenic plants with kanamycin. It is used for co-expression of the mitochondria transformation unit with the MTS-binding protein mLTRASi in the plant cell.
The mitochondria transformation unit is made up the following components: NtmLFS1 and NtmRFS1 are homologous to two adjacent sequences in the tobacco mitochondrial mitochondria non-coding sequences (position 292641-293235 and 293262-293835, respectively), the GFP gene is placed under the control of Arabidopsis mitochondria ATP6 promoter AtmATP6 PRO and the tobacco ATP6 terminator NtmATP6 TER. PBD (primer-binding domain) is designed to capture the plant mitochondria tRNA-fMet to initiate reverse transcription, LTRBM is based on the LtrB intron sequence from lactococcus lactis and serves as the mitochondria translocation sequence (MTS) into which the first six components were cloned, between the AscI and NotI restriction sites. The whole mitochondria transformation unit was placed under the control of the 35S promoter and the nos terminator.
The second cassette is for expression of the MTS-binding protein MLTRASi placed under the control of the AtUBI3 promoter and ags terminator.
M28 Construct
The pSOUP vector (EU048870) carrying T-DNA from the pGreen0179 vector (EU048866) was used as a backbone and enables selection of transgenic plants with Hygromycin. It is used for expression of the mitochondria-targeted reverse transcriptase-RNaseH protein (mRTRHi-Ty) under the control of the TAF2 promoter and ags terminator.
FIG. 4: M22 construct
The binary vector pGreen0029 was used as a backbone and enables selection of transgenic plants with kanamycin. It is used for co-expression of the mitochondria transformation unit with the MTS-binding protein mLTRASi in the plant cell.
The mitochondria transformation unit is made up the following components: NtmLFS4 and NtmRFS4 correspond to Nicotiana tabacum mitochondria sequences position 24888-24579 and 24578-24269 respectively (on the complementary strand). NtmLFS4 corresponds to the 5′ end of the gene coding for ATP6 and can be used for translational fusion with any gene of interest, promoter activity is provided by the ATP6 promoter upstream of NtmLFS4 on the tobacco mitochondrial genome and termination of transcription is achieved with the ATP6 terminator sequence within NtmRFS4. The GFP gene was fused to NtmLFS4 and cloned upstream of NtmRFS4 and PBD. LTRBM is based on the LtrB intron sequence from lactococcus lactis and serves as the mitochondria translocation sequence (MTS) into which the first four components were cloned, between the AscI and NotI restriction sites. The whole mitochondria transformation unit was placed under the control of the 35S promoter and the nos terminator.
The second cassette is for expression of the MTS-binding protein MLTRASi placed under the control of the AtUBI3 promoter and ags terminator.
FIG. 5: M24 construct
The binary vector pGreen0029 was used as a backbone and enables selection of transgenic plants with kanamycin. It is used for co-expression of the mitochondria transformation unit with the MTS-binding protein mLTRASi in the plant cell.
The mitochondria transformation unit is made up the following components: NtmLFS3 and NtmRFS3 correspond to Nicotiana tabacum mitochondria sequences position 85896-86331 and 86332-86860, respectively. the PCFM gene is based on the CMS-inducing PCF gene from petunia mitochondria, PBD (primer-binding domain) is designed to capture the plant mitochondria tRNA-fMet to initiate reverse transcription. LTRBM is based on the LtrB intron sequence from lactococcus lactis and serves as the mitochondria translocation sequence (MTS) into which the first four components were cloned, between the AscI and NotI restriction sites. The whole mitochondria transformation unit was placed under the control of the 35S promoter and the nos terminator.
The second cassette is for expression of the MTS-binding protein MLTRASi placed under the control of the AtUBI3 promoter and ags terminator
FIG. 6: M27 construct
The binary vector pGreen0029 was used as a backbone and enables selection of transgenic plants with kanamycin. It is used for co-expression of the mitochondria transformation unit with the MTS-binding protein MLTRASi in the plant cell.
The mitochondria transformation unit is made up five components: AtmLFS5 and AtmRFS5 are homologous to two adjacent sequences in the Arabidopsis mitochondrial (position 344225-344571 and 344572-344926, respectively), the PCFM gene is based on the CMS-inducing PCF gene from petunia mitochondria, PBD (primer-binding domain) is designed to capture the plant mitochondria tRNA-fMet to initiate reverse transcription, LTRBM is based on the LtrB intron sequence from lactococcus lactis and serves as the mitochondria translocation sequence (MTS) into which the first four components were cloned, between the AscI and NotI restriction sites. The whole mitochondria transformation unit was placed under the control of the 35S promoter and the nos terminator.
The second cassette is for expression of the MTS-binding protein MLTRASi placed under the control of the AtUBI3 promoter and ags terminator.
M28 Construct
The pSOUP vector (EU048870) carrying T-DNA from the pGreen0179 vector (EU048866) was used as a backbone and enables selection of transgenic plants with Hygromycin. It is used for expression of the mitochondria-targeted reverse transcriptase-RNaseH protein (mRTRHi-Ty) under the control of the TAF2 promoter and ags terminator
FIG. 7: Aborted pollen phenotype in tobacco plants transformed with the CMS-inducing pcf gene from petunia mitochondria
(A,B) Pollen from wild type (WT) plants.
(C,D) Pollen from transgenic tobacco line PCFM1, transformed with the M24 vector carrying the CMS-inducing PCF orf from petunia, showing 90% of aborted pollen.
FIG. 8: Modifications of the mitochondria transformation cassette were made by designing primer binding domain and positioning of building blocks on the transgene cassette.
MTU—mitochondria transformation unit; MTS—mitochondria translocation sequence; PDB-MIT—primer binding domain designed for reverse transcription in the mitochondria using tRNA-Met from mitochondria; PBD-CYT—primer binding domain designed for reverse transcription, in the cytoplasm using cytoplasmic tRNA-Met.
The modifications detailed in Example section 1B hereinafter and corresponding figures include modifications of the use of PBD for the binding of cytoplasmic tRNA-Met as primer. As one modification MTS can be located at both the 5′- and 3′-ends of the transformation cassette, such as in the case with the LtrB intron. The transgene cassette is inserted inside of the LtrB intron (domain IV). The PDB-MIT is located downstream of the LtrB 3′-end of the cassette (MTS-3′), so that the LtrA protein is able to function as both a translocation protein and reverse transcriptase. The LtrA protein has three major functions: (1) as a maturase (it binds to LtrB RNA and stabilises the secondary structure of the RNA, and assists splicing); (2) as an endonuclease (it induces single-stranded DNA breaks on target site); and (3) as a reverse transcriptase (it performs reverse transcription of the intron RNA after insertion of the LtrB intron RNA into the donor site).
The LtrA protein is unable to perform the reverse transcription reaction efficiently if the PBD-CYT is located adjacent to and in front of a mitochondrion translocation sequence at the 3′-end of the MTU (MTS-3′) as in FIG. 8(B), but can efficiently reverse transcribe RNA if the PBD is located downstream of a chloroplast translocation sequence (MTS-3′) as shown in FIG. 8A. Such a positioning or the combination of components of the transformation cassette as shown in FIG. 8(A) allows both the translocation of the MTU into the mitochondrion and reverse transcription of the MTU by the LtrA protein. Thus, by positioning of the MTS components and of the PBD-MIT as shown in FIG. 8(A) the procedure of transformation is simplified since there is no requirement to co-deliver another gene to provide a reverse transcriptase function.
A similar simplification of the procedure is achieved if a PBD-CYT is used, since there is a significant amount of native endogenous reverse transcriptase in the cytoplasm, and reverse transcription is initiated by endogenous reverse transcriptase using cytoplasmic tRNA-Met. This also eliminates the necessity for the co-delivery of another gene for reverse transcription in the mitochondria.
The case in FIG. 8A and FIG. 8B is attributed to the LtrB intron.
FIG. 9: Tobacco mitochondria transformation constructs

    
    
        (A) M43 construct: PBD-MIT was fused to the 3′ end of the LtrB intron
        (B) M44 construct: PBD-CYT was fused to MTU
    
    


PBD-MIT: Primer binding domain designed to anneal with t-RNAmet from mitochondria to initiate reverse transcription. LTRB5, LTRB3: 5′ and 3′ sequences of the LTRB intron, respectively. NtmLFS3: tobacco mitochondria left flanking sequence. NtmRFS3: tobacco mitochondria left flanking sequence. PCFM: CMS-inducing open reading frame from petunia. 35S pro: promoter from CaMV (Cauliflower mosaic virus). TAF2 Pro: Arabidopsis promoter. 1-beta MTP: mitochondria transit peptide from ATPase 1 beta subunit. LTRASii: sequence coding for the LTRA protein. Ags ter and nos ter: transcription terminator sequences from agrobactérium. KanR: NPTII gene for kanamycin resistance.
FIG. 10: Rice mitochondria transformation constructs

    
    
        (A) M45 construct: PBD-MIT was fused to the 3′ end of the LtrB intron
        (B) M46 construct: PBD-CYT was fused to MTU
    
    


PBD-MIT: Primer binding domain designed to anneal with t-RNA Met from mitochondria to initiate reverse transcription. LTRB5, LTRB3: 5′ and 3′ sequences of the LTRB intron, respectively. osLFS3: rice mitochondria left flanking sequence. osRFS3: rice mitochondria left flanking sequence. PCFM: CMS-inducing open reading frame from petunia. 35S pro: promoter from CaMV (Cauliflower mosaic virus). Act1 Pro: rice promoter from the actin gene. 1-beta MTP: mitochondria transit peptide from ATPase 1 beta subunit. LTRASii: sequence coding for the LTRA protein. Ags ter and nos ter: transcription terminator sequences from agrobactérium. KanR: NPTII gene for kanamycin resistance.



EXPERIMENTAL SECTION 1A
A Novel Approach for Plant Mitochondria Transformation
A new method for transformation of the plant mitochondrial genome comprises
(1) a plant mitochondria transformation unit (MTU) consisting of 3 major domains:


    
    
        (i) a plant mitochondria translocation sequence (MTS),
        (ii) a plant mitochondria transgene cassette
        (iii) a primer binding domain (PBD) which uses plant mitochondria tRNA-fMet or any other mitochondrial RNAs as a primer for reverse transcription;

(2) a reverse Transcriptase-RNase H(RT-RH) from retrotransposons, retroviruses, intron maturases or any protein with reverse transcription activity is fused to a plant mitochondria transit peptide for targeting into the plant mitochondria;

(3) an RNA binding protein that binds to the plant mitochondria translocation sequence (MTS), fused to a plant mitochondria transit peptide (FIG. 1).

Technology Rationale

    
    


The process of plant mitochondria transformation comprises two steps (see FIG. 2).
(1) Targeting of an RNA-Protein Complex to the Plant Mitochondria
The mitochondria transformation construct is expressed from the nucleus using a constitutive promoter. After delivery of the mitochondria transformation construct into the plant cell a strong expression of the RNA which contains the mitochondria translocation sequence (MTS), transgene cassette and primer binding domain (PBD) is achieved. The MTS binding protein (MTS-BP) fused to a plant mitochondria transit peptide, is also expressed on co-delivery from the same or a different nuclear transformation vector. It is used to bind to MTS and facilitate the translocation of the MTU RNA into the mitochondria.
Once the plant mitochondria transformation vector is presented in the plant cell via nuclear transformation, the mitochondria will then be permanently bombarded by the expressed MTS-BP/MTU RNA complex. Such stable and continuous pumping of the complex into the targeted organelle is a prerequisite for achieving a high efficiency of organelle transformation. The technology exploits the finding that the plant mitochondria transit sequence is sufficient to permit the whole MTS-BP/MTU RNA complex to be then taken up by the mitochondria.
The plant mitochondrial translocation sequences (MTS) can be selected from a number of RNA sequences such as mitoviruses, viral RNAs (including viral coat protein binding domains), group I and group II intron RNAs, retrotransposon primer binding sites, or any RNA that harbors a domain recognised by RNA binding proteins.
The MTS-binding protein can be any RNA binding protein that recognises and binds to specific RNA domains.
The plant mitochondrial transit peptide can be derived from any mitochondria-targeted proteins.
The fusion of MTS-BP to a mitochondrial transit peptide enables this protein to act as a carrier of RNA molecules into the plant mitochondria provided that these RNA molecules carry the corresponding MTS domain.
(2) Reverse Transcription of the Transgene Cassette and Insertion into the Plant Mitochondria Genome.
Once the MTU RNA is inside the mitochondria, its' primer binding domain (PBD) captures tRNA-fMet as a primer to form a template ready for reverse transcription. Simultaneously, a reverse transcriptase (RT-RH) fused to a plant mitochondria transit peptide is expressed from the nucleus using a constitutive promoter. It is targeted into the mitochondria where it facilitates reverse transcription of the MTU-RNA into single stranded DNA.
This is followed by insertion of the reverse transcribed cassette into the plant mitochondrial genome using homologous recombination between sequences flanking the transgene cassette (LFS, RFS) and the homologous regions in the plant mitochondria genome.
The Primer binding domain (PBD) is designed to capture the RT-RH protein and plant mitochondria tRNA-fMet (or any other plant mitochondrial tRNAs) as a primer, to initiate reverse transcription of the MTU RNA, carrying the plant mitochondria transgene cassette, into single-stranded DNA.
Once the population of organelle genomes has been transformed in the initial plant line, the nuclear encoded transgenes are no longer required and can then be removed through segregation in subsequent plant generations, leaving a clean organelle transformed plant line (FIG. 2).
Materials and Methods.
Part 1 ̃Nucleic Acid Sequence Information
1. Preparation of a Group II Intron-Based Plant Mitochondria Translocation Sequence (MTS).
The LtrB intron from Lactococcus lactis lacking the gene coding for LTRA (intron-encoded maturase) was synthesised by a commercial DNA synthesis provider (Bio S&T Inc., Montreal (Quebec), Canada). Potential splicing donor and acceptor sites were mutagenised to prevent splicing for optimum accumulation of the groupII intron RNA in plant cytoplasm, the resulting group II intron sequence was named LtrBM.
The domain for insertion of the plant mitochondria transgene cassette (AscI-MluI-NotI sites) is underlined and shown in bold letters.
LtrBM Intron Sequence







SEQ ID NO. 1


GGATCCCTCGAGGTGCGCCCAGATAGGGTGTTAAGTCAAGTAGTTTA


 


AGGTACTACTCAGTAAGATAACACTGAAAACAGCCAACCTAACCGAA


 


AAGCGAAAGCTGATACGGGAACAGAGCACGGTTGGAAAGCGATGAGT


 


TAGCTAAAGACAATCGGCTACGACTGAGTCGCAATGTTAATCAGATA


 


TAAGCTATAAGTTGTGTTTACTGAACGCAAGTTTCTAATTTCGGTTA


 


TGTGTCGATAGAGGAAAGTGTCTGAAACCTCTAGTACAAAGAAAGCT


 


AAGTTATGGTTGTGGACTTAGCTGTTATCACCACATTTGTACAATCT


 


GTTGGAGAACCAATGGGAACGAAACGAAAGCGATGGCGAGAATCTGA


 


ATTTACCAAGACTTAACACTAACTGGGGATAGCCTAAACAAGAATGC


 


CTAATAGAAAGGAGGAAAAAGGCTATAGCACTAGAGCTTGAAAATCT


 


TGCAAGGCTACGGAGTAGTCGTAGTAGTCTGAGAAGGCTAACGGCCT


 


TTACATGGCAAAGGGCTACAGTTATTGTGTACTAAAATTAAAAATTG


 


ATTAGGGAGGAAAACCTCAAAATGAAACCAACAATGGCAATTTTAGA


 


AAGAATCAGTAAAAATTCACAAGAAAATATAGACGAAGTTTTTACAA


 


GACTTTATCGTTATCTTTTACGTCCTGATATTTATTACGTGGCGGGC


 


GCGCCACGCGTGCGGCCGCTGGGAAATGGCAATGATAGCGAAAGAAC


 


CTAAAACTCTGGTTCTATGCTTTCATTGTCATCGTCACGTGATTCAT


 


AAACACAAGTGAATTTTTACGAACGAACAATAACAGAGCCGTATACT


 


CCGAGAGGGGTACGTACGGTTCCCGAAGAGGGTGGTGCAAACCAGTC


 


ACAGTAATGTGAACAAGGCGGTACCTCCCTACTTCACCATATCATTT


 


TTAATTCTACGAATCTTTATACTGGCAAACAATTTGACTG






2. Mitochondria Transgene Cassettes

Positions of the various mitochondria sequences described below are derived from GenBank sequence accession numbers NC_006581 (Nicotiana tabacum mitochondrion) and NC_001284 (Arabidopsis thaliana mitochondrion).
2.1 Left and Right Flanking Sequences Used for Homologous Recombination
The mitochondria transgene cassette contains left and right flanking sequences (LFS and RFS) for insertion of the whole cassette into the mitochondrial genome using homologous recombination.
LFS and RFS sequences were amplified from coding and non-coding sequences of the mitochondrial genome of Nicotiana tabacum (NtmLFS, NtmRFS) and Arabidopsis Thaliana (AtmLFS, AtmRFS) using the primers described below.
2.1.1 NtmLFS1 and NtmRFS1, corresponding to corresponding to Nicotiana tabacum mitochondria non-coding sequences (position 292641-293235 and 293262-293835, respectively) were amplified from tobacco total cellular DNA using the following primers:
NtmLFS1:









IM101



SEQ ID NO. 2



GCGGGCGCGCCTATTACTCTCGGTCCTTGTTC


 



IM102



SEQ ID NO. 3



GCGGAGCTCTACCCTTTAAGACTCAATTACATCGAG






NTmRFS1:










IM103



SEQ ID NO. 4



GCATGCATTGCATAAGTAATCTCTTTTCTTATGAG


 



IM104



SEQ ID NO. 5



ACTAGTAAGGGGATTTGCCACATCGTTG






NtmLFS1 sequence:








SEQ ID NO. 6


TATTACTCTCGGTCCTTGTTCTTGGTCTCTGTGAAAGATCCAGTCGA


 


TGGGAATGAATCCATGTTCAAATCTTATTACCGGGTTCGATTACGGG


 


AAGGAAATAGAGAAGGTAAGGGACCGCTTTCCTTGTTCAAGCCGGTA


 


TTGTTTGAGTAAGTAGTAAGTAAGTGAGAAGTGGTGAATTGGCCAGG


 


AGGAATAAAGCTTATTTCAAGTACTAATAAAAGCATTCATTACAAAC


 


TCTTGTGCTCACTTATCCCAAGTATAGGATGTTTTCCCTGAGCCTGT


 


CTGTGTTGAATACGCTTTTTCCGTGTAGAATAGAGATTCTCTCTAAG


 


GTTGATAGAATATACGTTTTCTTTCTCTGATTAAAGGTTGTCCAAAG


 


AGGACTAAGAGACAGATGCTGTGCTTGCAAGTAAGCTTCAGCCAAGC


 


ATCAGATAAACCAAGTTCGGGTTGGGAAAAGGGCTATTTACCCCAGC


 


AATATAGAATAATTATTACCCCCAGCACATCCCCAAATGAGAGCATC


 


GTCTTTACCCCTAGAAAAGGTGCGATGTAATTTCCTGGTTCGATTAC


 


ATTGCTCGATGTAATTGAGTCTTAAAGGGTAGAGCTC






NtmRFS1 sequence:








SEQ ID NO. 7


ATTGCATAAGTAATCTCCTTTCTTATGAGAACTACGAATCATCCTCA


 


TGAATAAGCTCTACTCTACCTTAAGGAGATGTGGAGGCAATAGGTCC


 


CGTGCAGCTTTAACTAACTCTACTCCTCCATACGCCTATCCTTTAGT


 


TTAGTGGGCCAGGTCCTCCAGCCTTCCATTAGCTTTCGATTTAGTTT


 


GCATTCAAAGTCTTGGAATGCGAGCTTATGTGCTTTCAGGTATAGGC


 


ACCATTCGCCTGACTTTCTTGAAGTCCTAGGATTCTCCCCTAGTATT


 


CCATTCTCTCCCCCTCTCGGCCTTGCTTTCATTCCTGTCTCATTTGA


 


AATTGCTCCTAAGGCAGGGAGTCTTCTCGAAGCTGTCTAAGTCTTGT


 


AAGGCTCCTATATCTATATATAGAGAGGTCATGGTATGGAGGGAGGA


 


TTTCTACGCGCAACATCGTGGTTGGGGCATTCCTCCTTCTTTTAAAA


 


GAAGACTAGAGGACGAAAGAAGAAGCTCTTACATCGGATAAAGCCTA


 


ATTCCACTGTCCTTTGAAGATTGGAAGATAGTGAAGGCCGACTTCCT


 


TTTTAAAGATCACTCAACGATGTGGCAAATCCCCTTACTAGT






2.1.2 NtmLFS3 and NtmRFS3, corresponding to Nicotiana tabacum mitochondria sequences (position 85896-86331 and 86332-86860, respectively) were amplified from tobacco total cellular DNA using the following primers:
NtmLFS3









IM263
GGCGCGCCAGCAGATTTCCTCCCTCTATC
SEQ ID NO. 8


 


IM264
GCATGCAGATCGACGACGGAACGAAGAAC
SEQ ID NO. 9






NtmRFS3










IM265
TCTAGATCCAATTTCTTCCGGTATGC
SEQ ID NO. 10


 


IM375
CCGCGGTACGGTCCGTGCGCCGTT
SEQ ID NO. 11






NtmLFS3 Sequence:








SEQ ID NO. 12


AGCAGATTTCCTCCCTCTATCAACTCCTTTTTTATGGTCGGGAGGAT


 


CCACAATTCTTCATTGATCCACAAGACCTGGATTCCATACTGAGGGT


 


GCACCTTGAACCCTTAGAATTCAATCACCCTGCTCTATGCCAGGTCT


 


TAGAAAGTCTATGTGTCGAGAAGCATGATTCCCCTTTTTATCAAGAT


 


GTAAAAATGGCTCAAGCGCATCATTTTCGTGGCTTTATAAACTTAAA


 


GCACCAAGCGAAATTGGAAATGCAACATCGCCTAGAGTTAGGAGAGG


 


TATGGAAATCTCTTGAGAGAAGGAACGCTTTTCTAAGCCAGGAAAAC


 


GCCTCTCTAAGAGAAAAACTTTTAATTCTCGACAGGGAAGCCCCATA


 


GAAATTCTTCTTTGTTGTGTTGCTATCCTAAAATTGCGTTCTTCGTT


 


CCGTCGTCGATCT






NtmRFS3 Sequence:








SEQ ID NO. 13


TCTAGATCCAATTTCTTCCGGTATGCCGCTCCGCCAGCAAGGAGCGA


 


AAGAACCAAGTTTTCTGTGGTGATGTCAGAATTTGCACCTATTTGTA


 


TCTATTTAGTGATCAGTCCGCTAGTTTCTTTGCTCCCACTCGGTCTT


 


CCTTTTCTATTTTCTTCCAATTCTTCGACCTATCCAGAAAAATTGTC


 


GGCCTACGAATGTGGTTTCGATCCTTCCGGTGATGCCAGAAGTCGTT


 


TTGATATAAGATTTTATCTTGTTTCCATTTTATTTATTATTCCTGAT


 


CCGGAAGTAACCTTTTCCTTTCCTTGGGCAGTACCTCCCAACAAGAT


 


TGATCCGTTTGGATCTTGGTCCATGATGGCCTTTTTATTGATTTTGA


 


CGATTGGATCTCTCTATGAATGGAAAAGGGGTGCTTCGGATCGGGAG


 


TAACCACTAGTGAGAGGGCAAAAATTGGGGGGAAGGACAAAGGAAAG


 


AGCGATGCCTACATTAAATCAATTGATTCGTCATGGTAGAGAAGAAA


 


AACGGCGCACGGACCGTA






2.1.3 NtmLFS4 and NtmRFS4 corresponding to Nicotiana tabacum mitochondria sequences position 24888-24579 and 24578-24269 respectively (on the complementary strand).

NtmLFS4 corresponds to the 5′ end of the gene coding for ATP6 and can be used for translational fusion with any gene of interest, promoter activity is provided by the ATP6 promoter upstream of NtmLFS4 on the tobacco mitochondrial genome and termination of transcription is achieved with the ATP6 terminator sequence within NtmRFS4. Any plant mitochondrial coding sequence can be used instead of ATP6 to achieve expression of any gene of interest.
NtmLFS4 and NtmRFS4 were amplified from tobacco total cellular DNA using the following primers:
NtmLFS4









IM376
GGCGCGCCAGGGTATGATACCTTATAGCT
SEQ ID NO. 14


 


IM287
CTCGAGTGAGACTCGCTTTTGTTC
SEQ ID NO. 15






NtmRFS4










IM289
GAGCTCATGGGTATACTTAGTCGTGG
SEQ ID NO. 16


 


IM377
CCGCGGCTGAGATAGCTCCGTAAACTAAT
SEQ ID NO. 17






NtmLFS4 Sequence:








SEQ ID NO. 18


CCAGGGTATGATACCTTATAGCTTCACAGTTACAAGTCATTTTCTCA


 


TTACTTTGGGTCTCTCATTTTCTATTTTTATTGGCATTACTATAGTG


 


GGATTTCAAAAAAATGGGCTTCATTTTTTAAGCTTCTTATTACCTGC


 


AGGAGTCCCACTGCCATTAGCACCTTTTTTAGTACTCCTTGAGCTAA


 


TCCCTTATTGTTTTCGAGCATTAAGCTCAGGAATACGTTTATTTGCT


 


AATATGATGGCCGGTCATAGTTCAGTAAAGATTTTAAGTGGGTTCGC


 


TTGGACTATGCTATGTATGAATGATCTTTTATATTTCATAGGGGATC


 


TTGGTCCTTTATTTATAGTTCTTGCATTAACCGGTCTGGAATTAGGT


 


GTAGCTATATCACAAGCTCATGTTTCTACGATCTTAATCTGTATTTA


 


CTTGAATGATGCTATAAATCTTCATCAAAGTGCTTCTTTTTTTATAA


 


TTGAACAAAAGCGAGTCTCA






NtmRFS4 Sequence








SEQ ID NO. 19


ATGGGTATACTTAGTCGTGGAGCATTCCGAGTATTTGCTTTAGGGAT


 


CGTTCCTGCGCATCTCCTTACTTTATAGCAGTTATTGCTCCGGTTCC


 


AGAAGGTATAGCTCTCGCCTCAGCTTTTTCTTTGAAATCGGAGACTG


 


TTCCAATTTCCTACTGAGATAGGCAAGCGGAGGGAGAACTAGACGTA


 


TCTTGCTAGGCAAAGACAGGTTAGAATGGATAGCTCGCGGGTGGGAT


 


TGACGGGATAGATCACTATTGCAGAAGGAGGTAGAACCGGGGGAAGA


 


ATTATGGCTATAAAGGTCCTCGCCCTCTTAGGCACATGGTTCTAAAG


 


ATTAAATCTCAAAGCGGTACTAAAGATTAGGCAGAAGAAGAACTAGA


 


ACTAGAATTCTTCGCCCCTCCCCTTGTACCAAGAAGCAAGTTCAGAA


 


CATAAGGATAATGGGCTCGTCTATTATAAGTTATTAGTTTACGGAGC


 


TATCTCAG






2.1.4 AtmLFS5 and AtmRFS5 corresponding to Arabidopsis thaliana mitochondria sequences (position 344225-344571 and 344572-344926, respectively) were amplified from Arabidopsis total cellular DNA using the following primers:

AtmLFS5










SEQ ID NO. 20










IM398
GGCGCGCCGGGAGGAAGCTGGGCCAGTAGT



 









SEQ ID NO. 21










IM399
GCATGCGAAAAATAAAGAAAGAAGCAAAAGCCCAT






AtmRFS5










IM400
ATCGATATGCCGCTTCTTCGCCA
SEQ ID NO. 22


 


IM401
CCGCGGATTTTGTGCCCTATCACTTTAC
SEQ ID NO. 23






AtmLFS5 Sequence








SEQ ID NO. 24


GGGAGGAAGCTGGGCCAGTAGTCCCCTATCCATACAGGAGGGATGAA


 


ATGATTGGGGGGGATAGCGTAGAGGCGATAGAACGCCGCCTTCTGGC


 


GAAATACCCCGAAGGCTCTCCCTCTGCGGAGATCATAGAGATGGCCC


 


GAATAGAGGCCGAAGATCTATTCGAGATCAAAGCCCAAATCATCCAA


 


CGGATGGCTCTATATGACCCAACCGGCGATTGGATGGCGCGTGGGGC


 


TCGGGCCCTCGATAATCCGAGGACCACTAGTGGGGAAGAGTCCTTGG


 


AGCGTCTTTATGATATATGGAAGGACCTCCAAGAAACCGGGCCCCTC


 


TCGGACGAGTTTTCTCGTTTACAAGAGAAAGTATTCCTCAAGAAAGG


 


CGGCCCTGGGGGGGACCCTATCGCATAAGGTCTGCAAGCCTTTCGGG


 


ATGGGCTTTTGCTTCTTTCTTTATTTTTCG






AtmRFS5 Sequence







SEQ ID NO. 25


ATATGCCGCTTCTTCGCCAGCAAGGAGCGAGAAAACAAAGTGGGCTG


 


TAATGATGTCAGAATTTGCACCAATTTCTATCTATTTAGTGATTAGT


 


CTGCTAGTTTCTTTGATCCTACTCGGTGTTCCTTTTCCATTTGCTTC


 


CAATAGTTCTACCTACCCAGAAAAATTGTCGGCCTACGAATGTGGTT


 


TCGATCCTTCCGGTGATGCCAGAAGTCGTTTCGATATACGATTTTAT


 


CTTGTTTCAATTTTATTTTTAATCCCTGATCTGGAAGTAACCTTTTT


 


CTTTCCTTGGGCAGTACCTCCCAACAAGATTGATCTGTTTGGATTTT


 


GGTCCATGATGGCCTTTTTATTTATTTTGACGATTGGATTTCTATAT


 


GAATGGAAAAGGGGTGCTTCGGATCGGGAGTAAAGTGATAGGGCACA


 


AAAT






2.2 Plant Mitochondria Promoter and Terminator Sequences

2.2.1 ATP6 promoter sequences were amplified from total cellular DNA of Nicotiana tabacum (NtATP6-PRO) and Arabidopsis thaliana (AtATP6-PRO) using the following primers:

NtATP6-PRO










IM364
GGCGCGCCTCTAGTCGAATAGAGTATTAG
SEQ ID NO. 26


 


IM365
ATCTCGAGTGTGATTGAGATAAAAAGATTCC
SEQ ID NO. 27






AtATP6-PRO










SEQ ID NO. 28










IM346
CTGCATGCTCCTCTACTGAGTCAGTGACAG



 









SEQ ID NO. 29










IM347
ATTCTAGAATTGGATTAATTGATTTCAACAAAATG






NtATP6-PRO Sequence








SEQ ID NO. 30


CCTCTAGTCGAATAGAGTATTAGTCCGCTCCATTATATTCCCCATTATTT


 


CACTTTCTCGCTATTCGAAATATCATAAGAGAAGAAAGCTGGCAGGTTGG


 


ATCCTAGGGTAGATTCCTGCTGTTGAATGATCGACTAGCTTCCTCTTTAG


 


TTCTTTGATATTGGGTTCGTGTTCAGTGTACCGCTCTTTTTATATATGAA


 


ATTACTTCGTCCTTTTTTTTAGCCCTTTTTCGTTTGTCCATCTTTTTTTC


 


TCCCATGCTTTCCGTTGGTCAACAACCAACCAAAGTGCTCTATACTTCTT


 


CACTACTCGTACAGGCTTGACGGAGTTAAGCTGTATTGAGGGAATCTTTT


 


TATCTCAATCA






AtATP6-PRO Sequence








SEQ ID NO. 31


TCCTCTACTGAGTCAGTGACAGAAGTGCAGCAGCCAATAATACGTATATA


 


AGAAGAGGACTGCTTACGGGATCAAACTATCAATCTCATAAGAGAAGAAA


 


TCTCTATGCCCCCTTTTTCTTGGTTTTCTCCCATGCTTTTGTTGGTCAAC


 


AACCAACCACAACTTTCTATAGTTCTTCACTACTCCTAGAGGCTTGACGG


 


AGTGAAGCTGTCTGGAGGGAATCATTTTGTTGAAATCAATTAATCCAAT






2.2.2 ATP6 terminator sequence was amplified from total cellular DNA of Nicotiana tabacum (NtATP6-TER) using the following primers:










IM289
GAGCTCATGGGTATACTTAGTCGTGG
SEQ ID NO. 32


 


IM366
CCGCGGCGAGGACCTTTATAGCCATAATTC
SEQ ID NO. 33






NtATP6-TER Sequence








SEQ ID NO. 34


ATGGGTATACTTAGTCGTGGAGCATTCCGAGTATTTGCTTTAGGGATCGT


 


TCCTGCGCATCTCCTTACTTTATAGCAGTTATTGCTCCGGTTCCAGAAGG


 


TATAGCTCTCGCCTCAGCTTTTTCTTTGAAATCGGAGACTGTTCCAATTT


 


CCTACTGAGATAGGCAAGCGGAGGGAGAACTAGACGTATCTTGCTAGGCA


 


AAGACAGGTTAGAATGGATAGCTCGCGGGTGGGATTGACGGGATAGATCA


 


CTATTGCAGAAGGAGGTAGAACCGGGGGAAGAATTATGGCTATAAAGGTC


 


CTCG






2.3 Transgene Sequences

2.3.1 Green Fluorescent Protein (GFP) Sequence

The GFP gene was synthesised according to GenBank accession number XXU70496
GFP Sequence







SEQ ID NO. 35


ATGAGTAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGA


 


ATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTG


 


AAGGTGATGCAACATACGGAAAACTTACCCTTAAATTTATTTGCACTACT


 


GGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCACTTATGG


 


TGTTCAATGCTTTTCAAGATACCCAGATCATATGAAGCGGCACGACTTCT


 


TCAAGAGCGCCATGCCTGAGGGATACGTGCAGGAGAGGACCATCTCTTTC


 


AAGGACGACGGGAACTACAAGACACGTGCTGAAGTCAAGTTTGAGGGAGA


 


CACCCTCGTCAACAGGATCGAGCTTAAGGGAATCGATTTCAAGGAGGACG


 


GAAACATCCTCGGCCACAAGTTGGAATACAACTACAACTCCCACAACGTA


 


TACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAAT


 


TAGACACAACATTGAAGATGGAAGCGTTCAACTAGCAGACCATTATCAAC


 


AAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTAC


 


CTGTCCACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGAGAGACCA


 


CATGGTCCTTCTTGAGTTTGTAACAGCTGCTGGGATTACACATGGCATGG


 


ATGAACTATACAAATAA






2.3.2 Gene for Induction of Cytoplasmic Male Sterility

The sequence coding for the PCFM gene was based on the petunia mitochondria PCF gene responsible for induction of CMS. It comprises a promoter, open reading frame and 3′ untranslated sequence. It was modified to remove putative splicing sites for optimum expression of the PCFM RNA in the cytoplasm on transit to the mitochondria.
PCFM was synthesised using a commercial DNA synthesis provider (Bio S&T Inc., Montreal (Quebec), Canada).
The location of mutagenised donor sites are underlined
PCFM Sequence







SEQ ID NO. 36


GAACTCAATGGGGCCAGTTATAGCATCCTGCTTCTTCTTACAAAAGAAAT


 


TTCATAAGATAAGAGAGATGAGGCAAAGAAGGAATTGATAGAGGTGCGGC


 


GAGAAGTTCAATACCTTCTTGATCGAGAAAATGTCCTTGCTTGTACTTCT


 


CTTTCTTTATCGAGATTGGGTTGGTGTTCAGTGTACCGCTTGTCTAGCCT


 


ATGCTTTGCATGAACATCTCAATGTCCAAGATAAAAAGAACGAGGGGAAG


 


AATCGACGAGGCCAGTGTTCTCGAAGAGAAAATCGTGATGGAAAAAGCGT


 


GAGGAGAATTCGAAACTCGAGATGTTAGAAGGTGCAAAATCAATGGGTGC


 


AGGAGCTGCTACAATTGCTTCAGCGGGAGCTGCTATCGGTATTGGAAACG


 


TCCTTAGTTCCTCGATTCATTCCGTTTTAGGGATACAAATAACAGACTTA


 


CATCACGATGTCTTTTTCTTCGTTATTCTGATTTTGGTTTTCGTATCATG


 


GATCTTGGGTCGCGCTTTATGGCATTTCCACTATAAAAAAAATCCAATCC


 


CGCAAAGGATTGTTCATGGAACTACTATCGAGATTCTTCGGACCTTATTT


 


CCTAGTATCATCCCTATGTTCATTGCTATACCATCATTTGCCCTGTATGG


 


GTATTCGGACTATAACAGTTCCGATGAACAGTCACTCACTTTTGACAGTT


 


ATACGATTCCAGAAGATGATCCAGAATTGGGTCAATCACGTTTATTAGAA


 


GTCGACAATAGAGTGGTTGTACCAGCAAACAGTTCTCTCCGTTTTATTGT


 


AACATCTGCGGCTGTACCTTCCTTAGGTGTCAAAGGTGATGCTGTGCCTT


 


CCTTAGGTGTCAAAGGTGATGCTGTGCCTTCCTTAGGTGTCAAAGGTGAT


 


GCTGTGCCTGGGCCTGGGCGGGTTTTTCAGACTTGGACCCGAGCTTTTGA


 


GCGTTTGGGCCTGTTGACGGTTGCCCATTGCGCCGGCACCGGAACATCAA


 


GCTCGGGCTCGGTAGTCAGTCTTCCACAGGACGAAATATGGGCCGCCCTT


 


GAGGGCGATCCCCAGGCCCTTCCGGAAGACGGGCAATTTCACGCCGTCGC


 


CCCTGAGGGGAATCCCCAGGCCCTTCCGGAAGACGGGCAATTTCACGCCG


 


TCGCCCCTGAGGGGAATCCCCAGGCCCTTCCGGAAGACGGGCAATTTCAC


 


GCCGTCGCCCCTGAGGGGAATCCCCAGGCCCTTCCGGAAGACGGGCAATT


 


TCACGCCATCGCCTTTGACCCTCTTATAGCAACACGGCAAGACGCGTGGA


 


ATACGCTACTTGTCTTGTTGCGGCGCAGCACCAAAATTGAGCCTAAGGCC


 


AATTTTGTTACTAAAGCAGGGGAAGATCTTGGTATAGATACCGCAGACCC


 


TGTTCGCCTTGACAAGTTAGTACGGGTACTGAACACGTATATCCAACTCG


 


CCCCATTAGAAAGCGGGAGAAAGGTCCTCCAAAACCTGAAAGCCACGATG


 


GCTGAATGGGAAAAGAACGGAAGGCCCTAAGTGGTGTCGTGTACTTTTTT


 


CAATTATAATTAAATAAAAGGAGGTTACCGAATTTACGCGGTGGCCCTTT


 


TATGTATGTTGCTGTCGTAAAGTTTCGTTCT






2.4 Primer Binding Domain for Reverse Transcription

A Primer Binding Domain (PBD) was designed to capture the plant mitochondria tRNA-fMet as described by Friant et al., (1998) to be used as a template for reverse transcription
PBD was constructed by overlapping PCR using the set of following primers:









IM374



SEQ ID NO. 37



TTCCGCGGCCTATCTCACATTCACCCAATTGTCA



 



IM368



SEQ ID NO. 38



TTAGAAGTATCCAATGCACAGTAGGTACCATGACAATTGGGTGAA



 



IM369



SEQ ID NO. 39



ATTGGATACTTCTAAGGAAGTCCACACAAATCAAGAACCATTAGA



 



IM370



SEQ ID NO. 40



CTCACATTCTTCTGTTTGGTTAGATGAAACGTCTAATGGTTCTTGA






PBD MIT








SEQ ID NO. 41


TATCTCACATTCACCCAATTGTCATGGTACCTACTGTGCATTGGATACTT


 


CTAAGGAAGTCCACACAAATCAAGAACCATTAGACGTTTCATCTAACCAA


 


ACAGAAGAATGTGAGAAGGCTTCCACTAAGGCTAACTCTCAACAGACAAC






3 Mitochondria Transit Peptide (mTP)

The sequence coding for the Mitochondrial ATPase 1β subunit transit peptide (1β-mTP) was amplified from total tobacco cellular DNA with the following primers:
Proteins translationally fused to 1β-mTP can be driven inside the plant mitochondria.









IM267
ATACTCGAGTCTCTCTCTACTCCTTTCAC
SEQ ID NO. 42


 


IM268
ATAGCATGCTGATGGCTGAGATGCCGGTG
SEQ ID NO. 43






1β-mTP Sequence







SEQ ID NO. 44


TCTCTCTCTACTCCTTTCACTCTCTCTCTAGCCAAACCCTCCACCATGGC


 


TTCTCGGAGGCTTCTCGCCTCTCTCCTCCGTCAATCGGCTCAACGTGGCG


 


GCGGTCTAATTTCCCGATCGTTAGGAAACTCCATCCCTAAATCCGCTTCA


 


CGCGCCTCTTCACGCGCATCCCCTAAGGGATTCCTCTTAAACCGCGCCGT


 


ACAGTACGCTACCTCCGCAGCGGCACCGGCATCTCAGCCATCA






4 Mitochondria-Targeted Reverse Transcriptase-RNaseH Protein

The reverse transcriptase-RNase H gene from the yeast Ty1-H3 retrotransposon (Boeke et al., Mol. Cellul. Biology (1988), 8: 1432-1442; bank accession No. M18706) was optimised for codon usage in plants and by insertion of 5 introns from the Arabidopsis genome (intron 1—from At1g04820, intron 2—from At2g29550, intron 3—from At1g31810, intron 4 and 5—from At1g09170). The gene was synthesised by a commercial DNA synthesis provider and fused to the sequence coding for the mitochondria transit peptide 1β-mTP. The resulting gene was named mRTRHi-Ty1. The introns are underlined and shown in bold letters. The sequence coding for 1β-mTP is in italics lower case.
mRTRHi-Ty1 Sequence







SEQ ID NO. 45


ctcgagtctctctctactcctttcactctctctctagccaaaccctccac


 


catggcttctcggaggcttctcgcctctctcctccgtcaatcggctcaac


 


gtggcggcggtctaatttcccgatcgttaggaaactccatccctaaatcc


 


gcttcacgcgcctcttcacgcgcatcccctaagggattcctcttaaaccg


 


cgccgtacagtacgctacctccgcagcggcaccggcatctcagccatcag


 


catgcATGAACAATTCATCCCACAACATCGTTCCTATCAAGACTCCAACT


 


ACTGTTTCTGAGCAGAACACTGAAGAATCTATCATCGCTGATCTTCCACT


 


TCCTGATCTTCCTCCAGAATCTCCTACTGAATTTCCTGATCCATTCAAAG


 


AACTTCCACCTATCAACTCAAGACAAACTAACTCTTCATTGGGCGGAATT


 


GGCGATTCTAATGCTTACACTACTATCAACTCTAAGAAGAGGTATTGTAG


 


CCAGCCTCAACCAGTCTTTTTGCTGTTACATTTTCTTGGGCTCATCTAAT


 


GTTATTTTCCTATTTTGTTTTCAGGTCACTTGAAGATAATGAAACTGAAA


 


TCAAAGTTTCTAGGGATACATGGAATACTAAGAATATGAGATCACTTGAA


 


CCTCCAAGATCTAAGAAGAGAATCCATCTTATTGCAGCTGTTAAAGCTGT


 


GAAATCAATCAAACCAATTAGAACAACTCTTAGATACGATGAAGCAATTA


 


CATACAACAAAGACATCAAGGAGAAGGAGAAATACATCGAGGCTTACCAC


 


AAAGAAGTTAACCAACTTCTTAAGATGAAAACTTGGGATACTGATGAATA


 


CTACGATAGAAAAGAGATTGACCCTAAGAGAGTTATCAACTCAATGTTCA


 


TCTTCAACAAGAAGAGAGACGGAACTCACAAAGCTAGATTCGTTGCAAGA


 


GGAGATATTCAGCATCCTGACACTTACGATTCAGGTAAGTATTCCAATGT


 


TCTTCGATTATGAGTCAATGTTGTTACTGTATCTGTCTCTGTGGTTTATT


 


GTTTCAGGCTTAGTTATTGATTAGTATTGAAACTTCACTCACATATTTTT


 


TTGTTTGTTTTCTGAATTGTGCAGGTATGCAATCTAATACTGTTCATCAC


 


TACGCATTGATGACATCTCTTTCACTTGCATTGGACAATAACTACTACAT


 


TACACAACTTGACATATCTTCTGCATACCTTTACGCTGATATCAAGGAGG


 


AGCTTTACATTAGACCTCCACCACATTTGGGAATGAATGATAAGTTGATC


 


CGTTTGAAGAAATCACTTTACGGATTGAAACAATCTGGAGCTAATTGGTA


 


CGAAACTATCAAATCATACCTTATTCAGCAATGCGGTATGGAGGAAGTTA


 


GGGGATGGTCATGCGTATTCAAGAACTCTCAAGTTACAATCTGCCTCTTC


 


GTTGATGATATGGTGCTCTTCTCTAAGAATCTTAACTCAAACAAGAGAAT


 


CATTGAGAAGTTGAAGATGCAATACGACACTAAGATCATCAACCTTGGAG


 


AATCTGATGAGGAAATTCAATACGACATTCTTGGATTGGAAATCAAATAC


 


CAAAGAGGTGAGTTATATTTAACAGCTCATCAGTTACTTAAACACTTTTT


 


GGGACAAGCAGTTCAAACTCATGTTCCAATCCTAAAATTAATTGCAATTC


 


ACAGGTAAGTACATGAAGTTGGGAATGGAAAACTCATTGACTGAGAAGAT


 


TCCTAAACTTAACGTTCCTTTGAATCCAAAGGGAAGAAAGCTCTCTGCTC


 


CAGGACAACCAGGACTTTACATTGACCAGGATGAACTTGAGATTGATGAG


 


GATGAATACAAGGAGAAAGTACACGAGATGCAGAAGTTGATTGGACTTGC


 


TTCATACGTTGGATACAAATTCAGATTCGACCTTCTTTACTACATCAACA


 


CACTTGCTCAGCATATACTTTTCCCATCTAGGCAAGTTCTTGACATGACA


 


TACGAGCTTATCCAATTCATGTGGGACACTAGAGACAAGCAACTCATATG


 


GCACAAGAACAAGCCTACAGAGCCAGATAACAAGCTCGTTGCAATCTCTG


 


ATGCTTCTTACGGAAACCAACCATACTACAAATCACAAATTGGAAACATC


 


TACTTGCTTAACGGAAAGGTACTTTTCTCAAAGACTTTACCTTATTGTGG


 


AATATTGAATTTTCTGAAAGACTTCACCTTATCTACATTTGTAATTTTAC


 


TATGGTAATCAGGTGATTGGAGGAAAGAGCACTAAGGCTTCACTTACATG


 


CACTTCAACTACTGAGGCAGAGATCCACGCTATATCAGAATCTGTACCAC


 


TTCTTAACAACCTTTCTTACCTTATCCAAGAGCTTAACAAGAAGCCAATC


 


ATCAAGGGACTTCTTACTGACTCAAGATCAACAATCTCTATCATTAAGTC


 


TACAAATGAAGAGAAATTCAGAAACAGATTCTTCGGAACAAAGGCAATGA


 


GACTTAGAGATGAAGTTTCAGGTAAGTATTAACTTACCAAATGATCAATA


 


TTATTTTGAAATGCAGGTTTTAGAATAATACTCTCTGCCGTTCTTGTTTA


 


TTTCCAGGTAACAACCTTTACGTTTACTACATCGAGACTAAGAAGAACAT


 


TGCTGACGTTATGACAAAGCCTCTTCCTATCAAGACCTTCAAGTTGCTTA


 


CTAACAAATGGATTCATTA






5 MTS-Binding Protein (MTS-BP)

The LtrA protein from Lactococcus lactis encoded by the LtrB intron is able to bind to the LtrB intron-based plant mitochondria translocation sequence (MTS) described in part 1 and therefore serves as a MTS-binding protein. The sequence of the LtrA protein was first optimised for codon usage in plants and 5 plant introns were inserted into the coding sequence to improve LtrA expression in plants. The introns 1, 2 4 are from Arabidopsis gene At5g01290, intron 3 and 5 were selected from Arabidopsis gene At5g43940. The gene was synthesised by commercial DNA synthesis provider and fused to the sequence coding for the mitochondria transit peptide 1β-mTP. The resulting gene was named mLTRASi. The mLTRASi protein is able to bind to RNA molecules carrying the LtrB intron MTS and transfer these RNAs into the plant mitochondria.
Plant introns inserted in the coding sequence of the LtrA gene are underlined and shown in bold letters. The sequence coding for 1β-mTP is in italics lower case.
mLTRASi Sequence:







SEQ ID NO. 46


ctcgagtctctctctactcctttcactctctctctagccaaaccctccac


 


catggcttctcggaggcttctcgcctctctcctccgtcaatcggctcaac


 


gtggcggcggtctaatttcccgatcgttaggaaactccatccctaaatcc


 


gcttcacgcgcctcttcacgcgcatcccctaagggattcctcttaaaccg


 


cgccgtacagtacgctacctccgcagcggcaccggcatctcagccatcag


 


catgcATGAAGCCAACAATGGCAATCCTCGAACGAATCTCTAAGAACTCA


 


CAGGAGAACATCGACGAGGTACAATAACCCATATATATGAATTGATTCAT


 


GTGTTACTCGTACTTGTTTGAATATGTTTGGAGCAAGTTTGATACTTTTG


 


GATGATGATATCGCAAATTCGTTATCTTTTTGGCGTTATAGGTCTTCACA


 


AGACTTTACCGTTACCTTCTCCGTCCTGACATCTACTACGTGGCATATCA


 


GAACCTCTACTCTAACAAGGGAGCTTCTACAAAGGGAATCCTCGATGATA


 


CAGCTGATGGATTCTCTGAGGAGAAGATCAAGAAGATCATCCAATCTTTG


 


AAGGACGGAACTTACTACCCTCAGCCTGTCCGAAGAATGTACATCGCAAA


 


GAAGAACTCTAAGAAGATGAGACCTCTTGGAATCCCAACTTTCACAGACA


 


AGTTGATCCAGGAGGCTGTGAGAATCATCCTTGAATCTATCTATGAGCCT


 


GTCTTCGAGGATGTGTCTCACGGTTTCCGACCTCAGCGAAGCTGTCACAC


 


AGCTTTGAAGACAATCAAGAGAGAGTTCGGAGGTAAATTATATGCTTTGC


 


CACTTCCTCAAAAGATCATTTTAGGTTCATTGGTATGTGGTTTTTTTCTT


 


AACAGGTGCAAGATGGTTCGTGGAGGGAGATATCAAGGGATGCTTCGATA


 


ACATCGACCACGTCACACTCATCGGACTCATCAACCTTAAGATCAAGGAT


 


ATGAAGATGAGCCAGTTGATCTACAAGTTCCTCAAGGCAGGTTACCTCGA


 


AAACTGGCAGTACCACAAGACTTACAGCGGAACACCTCAGGGCGGAATCC


 


TCTCTCCTCTCCTCGCTAACATCTATCTTCATGAATTGGACAAGTTCGTT


 


CTCCAACTCAAGATGAAGTTCGACCGAGAGAGTCCAGAGAGAATCACACC


 


TGAATACCGGGAGCTTCACAACGAGATCAAAAGAATCTCTCACCGTCTCA


 


AGAAGTTGGAGGGCGAGGAGAAGGCTAAGGTTCTCTTGGAATACCAGGAG


 


AAGAGGAAGAGGTTGCCTACACTCCCTTGTACATCACAAACAAACAAGGT


 


TCGTTCTCTCCATTTTCATTCGTTTGAGTCTGATTTAGTGTTTTGTGGTT


 


GATCTGAATCGATTTATTGTTGATTAGTGAATCAATTTGAGGCTGTGTCC


 


TAATGTTTTGACTTTTGATTACAGGTCTTGAAGTACGTCCGATACGCTGA


 


CGACTTCATCATCTCTGTTAAGGGAAGCAAGGAGGACTGTCAATGGATCA


 


AGGAGCAATTGAAGCTCTTCATCCATAACAAGCTCAAGATGGAATTGAGT


 


GAGGAGAAGACACTCATCACACATAGCAGTCAGCCTGCTCGTTTCCTCGG


 


ATACGACATCCGAGTCAGGAGAAGTGGAACTATCAAGCGATCTGGAAAGG


 


TTCAATTCTTTCTTTCACATTTGTACTTGTTCACTCGTTTTATTAATCCT


 


CTTTAGAATGGAGATTCTTACCTCTGTGTGGCCTTTGGCAGGTCAAGAAG


 


AGAACACTCAACGGGAGTGTGGAGCTTCTCATCCCTCTCCAAGACAAGAT


 


CCGTCAATTCATCTTCGACAAGAAGATCGCTATCCAGAAGAAGGATAGCT


 


CATGGTTCCCAGTTCACAGGAAGTACCTTATCCGTTCAACAGACTTGGAG


 


ATCATCACAATCTACAACTCTGAATTGAGAGGTAAGCTGCTACCTCAAAC


 


TTTCTAGTGCTTCCATATTTCCTTTCTTCTGCAAGGCAGAGAACCATTGT


 


GGTTAAGTGTTTTAAATTGTGAATGTATAGGTATCTGCAACTACTACGGT


 


CTCGCAAGTAACTTCAACCAGCTCAACTACTTCGCTTACCTTATGGAATA


 


CTCTTGCTTGAAGACTATCGCATCTAAGCATAAGGGAACACTCTCAAAGA


 


CCATCTCTATGTTCAAGGATGGAAGTGGTTCTTGGGGAATCCCTTACGAG


 


ATCAAGCAGGGGAAGCAGAGGAGATACTTCGCCAACTTCAGTGAATGCAA


 


ATCTCCTTACCAATTCACTGATGAGATCAGTCAAGCTCCTGTGCTTTACG


 


GAACGCTCGGAACACTCTTGAGAACAGACTTAAGGCTAAGTGTTGTGAGT


 


CTTTGTGGAACATCTGATGAGAACACATCTTACGAGATCCACCACGTCAA


 


CAAGGTCAAGAACCTTAAGGGAAAGGAGAAGTGGGAGATGGCAATGATCG


 


CTAAGCAGCGGAAGACTCTTGTTGTTTGCTTCCATTGTCATCGTCACGTG


 


ATCCATAAGCACAAGTGAACTAGTAA






6. Promoter and Terminator Sequences used for Expression of Nuclear Cassettes

6.1 Promoter Sequences

6.1.1 Arabidopsis Ubiquitin Promoter AtUbi3-PRO

The 5′ promoter region from Arabidopsis ubiquitin 3 gene was amplified with the following primers:







SEQ ID NO. 47








IM326
CGAAGCTTGAATTCTACCGGATTTGGAGCCAAGTC


 







SEQ ID NO. 48








IM327
AAGGATCCTCTAGATGTTTGGTGACCTGAAATAAAACAATAG






AtUbi3-PRO Sequence








SEQ ID NO. 49


TACCGGATTTGGAGCCAAGTCTCATAAACGCCATTGTGGAAGAAAGTCTT


 


GAGTTGGTGGTAATGTAACAGAGTAGTAAGAACAGAGAAGAGAGAGAGTG


 


TGAGATACATGAATTGTCGGGCAACAAAAATCCTGAACATCTTATTTTAG


 


CAAAGAGAAAGAGTTCCGAGTCTGTAGCAGAAGAGTGAGGAGAAATTTAA


 


GCTCTTGGACTTGTGAATTGTTCCGCCTCTTGAATACTTCTTCAATCCTC


 


ATATATTCTTCTTCTATGTTACCTGAAAACCGGCATTTAATCTCGCGGGT


 


TTATTCCGGTTCAACATTTTTTTTGTTTTGAGTTATTATCTGGGCTTAAT


 


AACGCAGGCCTGAAATAAATTCAAGGCCCAACTGTTTTTTTTTTTAAGAA


 


GTTGCTGTTAAAAAAAAAAAAAGGGAATTAACAACAACAACAAAAAAAGA


 


TAAAGAAAATAATAACAATTACTTTAATTGTAGACTAAAAAAACATAGAT


 


TTTATCATGAAAAAAAGAGAAAAGAAATAAAAACTTGGATCAAAAAAAAA


 


ACATACAGATCTTCTAATTATTAACTTTTCTTAAAAATTAGGTCCTTTTT


 


CCCAACAATTAGGTTTAGAGTTTTGGAATTAAACCAAAAAGATTGTTCTA


 


AAAAATACTCAAATTTGGTAGATAAGTTTCCTTATTTTAATTAGTCAATG


 


GTAGATACTTTTTTTTCTTTTCTTTATTAGAGTAGATTAGAATCTTTTAT


 


GCCAAGTATTGATAAATTAAATCAAGAAGATAAACTATCATAATCAACAT


 


GAAATTAAAAGAAAAATCTCATATATAGTATTAGTATTCTCTATATATAT


 


TATGATTGCTTATTCTTAATGGGTTGGGTTAACCAAGACATAGTCTTAAT


 


GGAAAGAATCTTTTTTGAACTTTTTCCTTATTGATTAAATTCTTCTATAG


 


AAAAGAAAGAAATTATTTGAGGAAAAGTATATACAAAAAGAAAAATAGAA


 


AAATGTCAGTGAAGCAGATGTAATGGATGACCTAATCCAACCACCACCAT


 


AGGATGTTTCTACTTGAGTCGGTCTTTTAAAAACGCACGGTGGAAAATAT


 


GACACGTATCATATGATTCCTTCCTTTAGTTTCGTGATAATAATCCTCAA


 


CTGATATCTTCCTTTTTTTGTTTTGGCTAAAGATATTTTATTCTCATTAA


 


TAGAAAAGACGGTTTTGGGCTTTTGGTTTGCGATATAAAGAAGACCTTCG


 


TGTGGAAGATAATAATTCATCCTTTCGTCTTTTTCTGACTCTTCAATCTC


 


TCCCAAAGCCTAAAGCGATCTCTGCAAATCTCTCGCGACTCTCTCTTTCA


 


AGGTATATTTTCTGATTCTTTTTGTTTTTGATTCGTATCTGATCTCCAAT


 


TTTTGTTATGTGGATTATTGAATCTTTTGTATAAATTGCTTTTGACAATA


 


TTGTTCGTTTCGTCAATCCAGCTTCTAAATTTTGTCCTGATTACTAAGAT


 


ATCGATTCGTAGTGTTTACATCTGTGTAATTTCTTGCTTGATTGTGAAAT


 


TAGGATTTTCAAGGACGATCTATTCAATTTTTGTGTTTTCTTTGTTCGAT


 


TCTCTCTGTTTTAGGTTTCTTATGTTTAGATCCGTTTCTCTTTGGTGTTG


 


TTTTGATTTCTCTTACGGCTTTTGATTTGGTATATGTTCGCTGATTGGTT


 


TCTACTTGTTCTATTGTTTTATTTCAGGTCACCAAACA






6.1.2 CaMV 35S Promoter

The 35S promoter from Cauliflower mosaic virus (35S-PRO) was synthesised based on GenBank accession number AF502128
35S-PRO Sequence







SEQ ID NO. 50


TTAGCCTTTTCAATTTCAGAAAGAATGCTAACCCACAGATGGTTAGAG


 


AGGCTTACGCAGCAGGTCTCATCAAGACGATCTACCCGAGCAATAATC


 


TCCAGGAAATCAAATACCTTCCCAAGAAGGTTAAAGATGCAGTCAAAA


 


GATTCAGGACTAACTGCATCAAGAACACAGAGAAAGATATATTTCTCA


 


AGATCAGAAGTACTATTCCAGTATGGACGATTCAAGGCTTGCTTCACA


 


AACCAAGGCAAGTAATAGAGATTGGAGTCTCTAAAAAGGTAGTTCCCA


 


CTGAATCAAAGGCCATGGAGTCAAAGATTCAAATAGAGGACCTAACAG


 


AACTCGCCGTAAAGACTGGCGAACAGTTCATACAGAGTCTCTTACGAC


 


TCAATGACAAGAAGAAAATCTTCGTCAACATGGTGGAGCACGACACAC


 


TTGTCTACTCCAAAAATATCAAAGATACAGTCTCAGAAGACCAAAGGG


 


CAATTGAGACTTTTCAACAAAGGGTAATATCCGGAAACCTCCTCGGAT


 


TCCATTGCCCAGCTATCTGTCACTTTATTGTGAAGATAGTGGAAAAGG


 


AAGGTGGCTCCTACAAATGCCATCATTGCGATAAAGGAAAGGCCATCG


 


TTGAAGATGCCTCTGCCGACAGTGGTCCCAAAGATGGACCCCCACCCA


 


CGAGGAGCATCGTGGAAAAAGAAGACGTTCCAACCACGTCTTCAAAGC


 


AAGTGGATTGATGTGATATCTCCACTGACGTAAGGGATGACGCACAAT


 


CCCACTATCCTTCGCAAGACCCTTCCTCTATATAAGGAAGTTCATTTC


 


ATTTGGAGAGAACACGGGGGAC






6.1.3 TAF2 Promoter Sequence
The 5′ untranslated region upstream of the TAF2 gene from Arabidopsis thaliana was synthesised based on sequence At1g73965 from the Arabidopsis genome, (www.arabidopsis.org).







SEQ ID NO. 51


GGTACCATGATCGCTTCATGTTTTTATCTAATTTGTTAGCATATTGAA


 


TGATTGATTTTCTTTTAATTTGGATATGTTGATTGTCTTGTTGCATCA


 


TCAATGTATGTTTTATTTAACACCGGAAGATCTTATGATGGGTTCATT


 


ACTTCATAATAATCTCCGAGTTCTACAAGACTACAACTTTCACGTGAC


 


TTTTACAGCGACAAAAAATGCATCTAGCGAAAATTAATCCACAACCTA


 


TGCATTTTTGTCACTCTTCACACGCGTATGTGCATAAATATATAGTAT


 


ATACTCGACAATCGATGCGTATGTGTACACAATTACCAAAACAATTAT


 


TTGAATATTCAGACATGGGTTGACATCACCAAGTAATATTCACAGTAT


 


CTGAAAACTATGTTTTGACATCCCTAAATAGTTTGACTAACCAGTTTA


 


ATATGAGAGCATTTGTAAGAGGCAAGAGCCATGGTTTTGTTGGCTCGT


 


TTAATATGCTCATTTAACCCCCCCAAAAAATACTATTAGATTTAAACG


 


TAAAAGAATTAACGAACACAAGAACTGCTAAAACAAAAAAAAATCAAT


 


GGCCGACATTTCATAGTTCATACATCACTAATACTAAAAGATGCATCA


 


TTTCACTAGGGTCTCATGAAATAGGAGTTGACATTTTTTTTTGTAACG


 


ACAGAAGTTGACATGTTAAGCATCAATTTTTTTAAGAGTGGATTATAC


 


TAGTTTTTTTTTTTTTTTTTAATGTATGGTATGATACAACAACAAAAA


 


CTATAAAATAGAAAAAGTCAGTGAAACCTCAAATTGAAGGAAAAACTT


 


TTGCACAAAAAGAGAGAGAGAGAGAAAGAATGTAAATCCAAATAAATG


 


GGCCTAATTGAGAATGCTTTAACTTTTTTTTTTTGGCTAAAAGAGAAT


 


GCTTTAACTAAGCCCATAAAATGAACATCAAACTCAAAGGGTAAGATT


 


AATACATTTAGAAAACAATAGCCGAATATTTAATAAGTTTAAGACATA


 


GAGGAGTTTTATGTAATTTAGGAACCGATCCATCGTTGGCTGTATAAA


 


AAGGTTACATCTCCGGCTAACATATCGGCAAAAAAGGAACCTCGAG






6.3 Terminator Sequences

6.3.1 Nos Terminator

The nos terminator fragment was synthesised based on GenBank sequence accession EU048864.
nos Terminator Sequence







SEQ ID NO. 52


TCTAGAGTCAAGCAGATCGTTCAAACATTTGGCAATAAAGTTTCTTAA


 


GATTGAATCCTGTTGCCGGTCTTGCGATGATTATCATATAATTTCTGT


 


TGAATTACGTGAAGCATGTAATAATTAACATGTAATGCATGACGTTAT


 


TTATGAGATGGGTTTTTATGATTAGAGTCCCGCAATTATACATTTAAT


 


ACGCGATAGAAAACAAAATATAGCGCGCAAACTAGGATAAATTATCGC


 


GCGCGGTGTCATCTATGTTACTAGATCGACCTGCAG






6.3.2 Ags Terminator

The agropine synthase polyA signal (ags terminator) was synthesized based on the GenBank sequence EU181145.
ags Terminator Sequence







SEQ ID NO. 53


GAATTAACAGAGGTGGATGGACAGACCCGTTCTTACACCGGACTGGGC


 


GCGGGATAGGATATTCAGATTGGGATGGGATTGAGCTTAAAGCCGGCG


 


CTGAGACCATGCTCAAGGTAGGCAATGTCCTCAGCGTCGAGCCCGGCA


 


TCTATGTCGAGGGCATTGGTGGAGCGCGCTTCGGGGATACCGTGCTTG


 


TAACTGAGACCGGATATGAGGCCCTCACTCCGCTTGATCTTGGCAAAG


 


ATATTTGACGCATTTATTAGTATGTGTTAATTTTCATTTGCAGTGCAG


 


TATTTTCTATTCGATCTTTATGTAATTCGTTACAATTAATAAATATTC


 


AAATCAGATTATTGACTGTCATTTGTATCAAATCGTGTTTAATGGATA


 


TTTTTATTATAATATTGATGAT






Part 2—Plant Transformation Methods and Vector Maps

Transformation of plants was carried out using constructs based on the pGreen0029 and pSOUP binary vectors (GenBank accession numbers EU0490266, EU048864 and EU048870) (Hellens et al, 2000, Plant Mol. Biol. 42: 819-832). The pSOUP-0179 vector is carrying the T-DNA from the pGreen0179 (GenBank accession number EU048866) vector into the pSOUP vector (GenBank accession number EU048870)
1. Transformation of Tobacco Plants
1.1. Transformation of tobacco plants was performed as described by Horsch et al (1985) (Science 227: 1229-1231) using Agrobacterium strain AGL1.
Plant transformants were selected on regeneration medium supplemented with Kanamycin 300 mg/l and/or Hygromycin 30 mg/l.
1.2 Vectors for Transformation of Tobacco Mitochondria
1.2.1 General Vectors for Transgene Expression into Mitochondria
Expression using a Heterologous Promoter
The ATP6 promoter region from Arabidopsis thaliana mitochondria (AtmATP6-PRO) can be used to direct expression of transgenes in tobacco mitochondria.
The gene coding for GFP was cloned between AtmATP6-PRO and the ATP6 terminator sequence from tobacco (NtmATP6-TER). This transgene expression construct was cloned between NtmLFS1 and NtmRFS1 upstream of PCD to form the mitochondria transformation unit (MTU). The mLTRASi sequence was placed under the control of the AtUbi3 promoter and ags terminator and cloned into the pGreen0029 together with the mitochondria transformation unit to generate the M21 vector (FIG. 3).
The mitochondria targeted reverse transcriptase-RNase H mRTRHi-Ty1 was placed under the control of the TAF2 promoter and ags terminator and cloned into the pSOUP-0179 vector to generate the M28 vector (FIG. 3).
The M21 and M28 constructs were co-transformed in Agrobacterium strain AGL1 and used for Nicotiana tabacum transformation.
Transgenic lines were recovered on selection medium supplemented with 300 mg/l of Kanamycin and/or 30 mg/l of Hygromycin:
Expression by Translational Fusion with a Native Mitochondrial Gene
NtmLFS4 corresponds to the 5′ end of the gene coding for ATP6 and can be used for translational fusion with any gene of interest, promoter activity is provided by the ATP6 promoter upstream of NtmLFS4 upon insertion in the tobacco mitochondrial genome and termination of transcription is achieved with the ATP6 terminator sequence within NtmRFS4. The gene coding for GFP was fused to NtmLFS4 and cloned together with NtmRFS4 and PBD into domain IV of the LtrBM intron to form the mitochondria transformation unit (MTU). The mLTRASi sequence was placed under the control of the AtUbi3 promoter and ags terminator and cloned into the pGreen0029 together with the mitochondria transformation unit to generate the M22 vector (FIG. 4).
The M22 and M28 constructs were co-transformed in Agrobacterium strain AGL1 and used for Nicotiana tabacum transformation.
Transgenic lines were recovered on selection medium supplemented with 300 mg/l of Kanamycin and/or 30 mg/l of Hygromycin.
1.2.2 Cytoplasmic-Male Sterility (CMS) Inducing Construct
The CMS-inducing tobacco mitochondria transformation unit containing NtmLFS3, PCFM, NtmLFS3 and primer binding domain (PBD) was inserted into domain IV of the LtrBM intron. The resulting DNA fragment was fused to the 35S promoter and nos terminator and introduced into the pGreen0029 binary vector. The mLTRASi sequence was placed under the control of the AtUbi3 promoter and ags terminator and cloned into the pGreen0029 together with the mitochondria transformation unit to generate the M24 vector (FIG. 5).
The M24 and M28 constructs were co-transformed in Agrobacterium strain AGL1 and used for Nicotiana tabacum transformation.
Transgenic lines were recovered on selection medium supplemented with 300 mg/l of Kanamycin and/or 30 mg/l of Hygromycin.
2. Transformation of Arabidopsis Thaliana 
2.1. Transformation of Arabidopsis plants was performed as described by Clough & Bent (Clough & Bent (1998) Plant Journal 16:735-743). The Agrobacterium tumefaciens strain GV3101 (Koncz & Schell (1986)—Mol Gen Genet. 204:383-396) was used for transformation. The resulting DNA fragment was fused to the 35S promoter and nos terminator and introduced into the pGreen0029 binary vector.

2.2 Vectors for Transformation of Arabidopsis thaliana Mitochondria

Cytoplasmic-Male Sterility (CMS) Inducing Construct

The CMS-inducing arabidopsis mitochondria transformation unit containing AtmLFS5, PCFM, AtmLFS5 and primer binding domain (PBD) was inserted into domain IV of the LtrBM intron. The resulting DNA fragment was fused to the 35S promoter and nos terminator and introduced into the pGreen0029 binary vector. The mLTRASi sequence was placed under the control of the AtUbi3 promoter and ags terminator and cloned into the pGreen0029 together with the mitochondria transformation unit to generate the M27 vector (FIG. 6).
The M27 and M28 constructs (FIG. 3) were co-transformed in Agrobacterium strain GV3101 and used for Arabidopsis (Col-0) transformation.
Transgenic lines were recovered on selection medium supplemented with 300 mg/l of Kanamycin and/or 30 mg/l of Hygromycin.
Part 3—Results
The transformation of Nicotiana tabacum and arabidopsis with our vectors containing transgene cassettes generated transgenic plants. In all cases we were able to detect insertion of the transgene cassette into the mitochondria genome using PCR amplification of junction regions.
Five independent transgenic lines were analysed for each construct. Molecular analyses including sequencing of insert junctions showed that there was correct insertion in the mitochondrial genome in 80% of transformed plants.
Furthermore, male sterile tobacco plants transformed with the CMS-inducing open reading frame PCF from petunia mitochondria were generated (FIG. 7).
EXPERIMENTAL SECTION 1B
Modifications of the mitochondria transformation method described in Experimental section 1A can be improved using PBD designed for reverse transcription in the cytoplasm or in mitochondria, and by re-positioning of the building blocks on the transformation cassette (FIG. 8).
A set of constructs was prepared for tobacco and rice transformation with LtrB intron (LtrB-MTS) as the MTS (FIG. 9-10). The positioning of the transgene cassette building blocks was designed as described in FIG. 8, A-B.
PBD-MIT was designed as described previously.
PBD-MIT







SEQ ID NO. 41


TATCTCACATTCACCCAATTGTCATGGTACCTACTGTGCATTGGATAC


 


TTCTAAGGAAGTCCACACAAATCAAGAACCATTAGACGTTTCATCTAA


 


CCAAACAGAAGAATGTGAGAAGGCTTCCACTAAGGCTAACTCTCAACA


 


GACAAC






The primer binding domain of the tobacco tnt1 retrotransposon was used as the PBD-CYT, and was amplified from genomic DNA of tobacco cv Petit Gerard using the following primers:









AS912
gccgcggctttattaccgtgaatatta
SEQ ID NO. 54


 


AS913
cgcggccgctctgataagtgcaacctgatt
SEQ ID NO. 55






PDB-CYT








SEQ ID NO. 56


CTTTATTACCGTGAATATTATTTTGGTAAGGGGTTTATTCCCAACAAC


 


TGGTATCAGAGCACAGGTTCTGCTCGTTCACTGAAATACTATTCACTG


 


TCGGTAGTACTATACTTGGTGAAAAATAAAAATGTCTGGAGTAAAGTA


 


CGAGGTAGCAAAATTCAATGGAGATAACGGTTTCTCAACATGGCAAAG


 


AAGGATGAGAGATCTGCTCATCCAACAAGGATTACACAAGGTTCTAGA


 


TGTTGATTCCAAAAAGCCTGATACCATGAAAGCTGAGGATTGGGCTGA


 


CTTGGATGAAAGAGCTGCTAGTGCAATCAGGTTGCACTTATCAGA






In the first case, PBD-MIT was fused to the 3′ end of the LtrB intron (FIG. 8A, FIG. 9A for tobacco and FIG. 10A for rice). As the LtrA protein possesses both LtrB-MTS-binding feature and reverse transcription activity it can fulfil both functions of (i) transgene RNA translocation into mitochondria and (ii) reverse transcription of the RNA cassette using mitochondrial tRNA-Met as a primer.
In the second case, PBD-CYT was fused to MTU (FIG. 8B, FIG. 9B for tobacco and FIG. 10B for rice), so that reverse transcription of the transgene cassette is initiated and performed by endogenous reverse transcriptases in the cytoplasm using cytoplasmic tRNA-Met. The LtrA protein serves as the MTS-binding protein for translocation of RNA:DNA complexes initiated by cytoplasmic reverse transcriptases, into the mitochondria.
Rice PCF Construct M45
Primers used to amplify the rice mitochondria left flanking sequence (osLFS) for insertion of the PCF open reading frame:










IM416 ggatccatatcgagccattgaagcag
SEQ ID NO. 57



 



IM417_gcatgctcaatcttgtcctttgg
SEQ ID NO. 58






osLFS








SEQ ID NO. 59


ggattcatatcgagccattgaagcagcgcgtcgggctacaatcgggca


 


attccatcgtgctatgagcggacaattccgaagaaattgtaagatatg


 


ggtaagagttctcgcagatcttcctattacggggaaacccgcagaagt


 


tcgaatgggaagaggaaaaggaaatcctacgggttggattgctcgtgt


 


gtccacgggacaaatcccatttgaaatggatggtgtgagtttgtcaaa


 


tgctcgacaagccgctagattagcggcgcataaaccatgttcgtcaac


 


caagtttgttcagtggtcgtaacgtaattggttagtggggaaaaaccg


 


ggccgggactcaaaagaatttggcgaagtgtttgttcctgaacgaggg


 


aagtggaaagacaaagagggatagggagctcgcctccttctttttttg


 


aatcgccgaaattgtacgacgacccttcttgttccaggcatacgactc


 


tgagacgtgacggtgtcacttttccggccoggtaaagtgacagttata


 


taaataagaataagaaagagaagcgtgatgttgtcagcaatcaaatta


 


tcgtaaatagatagtacggttgcgttgtttcaatttctgttcgtcggt


 


ccttgggttacgaaggtgtgggcttactaatacggagagggttccgaa


 


tgataaagtgtcatgaaagttcgtgaaagaatgttcttgtttttcgtt


 


ggaaaacccaacgccacggccacaaaacgaaaaagtctcccgtttgtt


 


ttgggagcagagctttaaaaggatatagttaccctatgatgagattta


 


gttcaacggataagaaggatagaagaaatatgctatttgctgctattc


 


catctatttgtgcattcagtgctgccgttcccccggccccaaaggaca


 


agattgagcatgc






Primers used to Amplify the Rice Mitochondria Left Flanking Sequence (osRFS) for Insertion of the PCF Open Reading Frame:











IM418 ttctagagtcgccgctatcacttt
SEQ ID NO. 60



 



IM419 ccgcggctaagactatagaatgttcc
SEQ ID NO. 61






osRFS








SEQ ID NO. 62


ttctagagtcgccgctatcactttttttggggggccaatcccgcgaag


 


agttatggaaagattttatagctcaattgaatgaagaaagtgaattca


 


tggacaacattttttttggtgtttacaacgcgagaaacggctatgaaa


 


gcgccacagttcttcagggaatacggatagatttagcgataaacggct


 


atgaaagtgcatttttgtcggaatttgcacctatttgtatctatttag


 


tgatcagtccgctagtttctttgattccactcggtgttccttttccat


 


ttgcttccaatagttcgacctatccagaaaaattgtcggcctacgaat


 


gtggtttcgatccctccggtgatgccagaagtcgtttcgatatacgat


 


tttatccggttcctattttatttattatccctgatctggaagtcacct


 


ttttttttccttgggcagtacctcctaacaagattgatctgtttggat


 


cttggtccatgatggcctttttattgattttgacgattggatttctct


 


atgaatggaaaaggggtgcttcggatcgggagtaaccactagtgaaag


 


ggcaaaggggggaaggacataggaaagagggatgcctacaaaaaatca


 


attgattcgtcatggtagagaagaaaaacagcgcacggaccgtactcg


 


agcttcggatcaatgtccccaaaagcaaggagtatgcctgcgtgtttc


 


gacgagaacaccgaaaaaacctaattcagctctacgtaagatagcaaa


 


agtacggttgagcaatcgacatgatatatttgctcacattccaggcga


 


aggtcataattcgcaggaacattctatagtcttagccgcggcc






The LtrA gene was driven by the actin1 rice promoter amplified using the following primers:










ARP1 gtcattcatatgcttgagaaga
SEQ ID NO. 63



 



ARP2 gcctacaaaaaagctccgcacg
SEQ ID NO. 64






Rice act1 Promoter Sequence








SEQ ID NO. 65


gtcattcatatgcttgagaagagagtcgggatagtccaaaataaaaca


 


aaggtaagattacctggtcaaaagtgaaaacatcagttaaaaggtggt


 


ataagtaaaatatcggtaataaaaggtggcccaaagtgaaatttactc


 


ttttctactattataaaaattgaggatgttttgtcggtactttgatac


 


gtcatttttgtatgaattggtttttaagtttattcgcgatttggaaat


 


gcatatctgtatttgagtcggtttttaagttcgttgcttttgtaaata


 


cagagggatttgtataagaaatatctttaaaaaacccatatgctaatt


 


tgacataatttttgagaaaaatatatattcaggcgaattccacaatga


 


acaataataagattaaaatagcttgcccccgttgcagcgatgggtatt


 


ttttctagtaaaataaaagataaacttagactcaaaacatttacaaaa


 


acaacccctaaagtcctaaagcccaaagtgctatgcacgatccatagc


 


aagcccagcccaacccaacccaacccaacccaccccagtgcagccaac


 


tggcaaatagtctccacccccggcactatcaccgtgagttgtccgcac


 


caccgcacgtctcgcagccaaaaaaaaaaaaagaaagaaaaaaaagaa


 


aaagaaaaacagcaggtgggtccgggtcgtgggggccggaaaagcgag


 


gaggatcgcgagcagcgacgaggcccggccctccctccgcttccaaag


 


aaacgccccccatcgccactatatacatacccccccctctcctcccat


 


ccccccaaccctaccaccaccaccaccaccacctcctcccccctcgct


 


gccggacgacgagctcctcccccctccccctccgccgccgccggtaac


 


caccccgcccctctcctctttctttctccgttttttttttcgtctogg


 


tctcgatctttggccttggtagtttgggtgggcgagagcggcttcgtc


 


gcccagatcggtgcgcgggaggggcgggatctcgcggctggcgtctcc


 


gggcgtgagtcggccoggatcctcgcggggaatggggctctoggatgt


 


agatctgcgatccgccgttgttgggggagatgatggggggtttaaaat


 


ttccgccatgctaaacaagatcaggaagaggggaaaagggcactatgg


 


tttatatttttatatatttctgctgcttcgtcaggcttagatgtgcta


 


gatcttctttctttcttctttttgtggtagaatttgaatccctcagca


 


ttgttcatcggtagtttttcttttcatgatttgtgacaaatgcagcct


 


cgtgcggagcttttttgtaggc






Transformation of Rice Immature Embryos.

Immature Embryo Excision

Day 1:

Remove milky/post-milky stage immature seeds from panicles (immature embryos 1-2 mm in size are desired).
Sterilize immature seeds: 50% sodium hypochlorite (12%)+1 drop of tween 20. Shake 10 min.
Rinse 3-5× in sterile deionised water. Drain off surplus water. Aliquot seeds (around 40) in sterile Petri dishes.
Set up a 60×15 mm Petri dish containing a 50% sodium hypochlorite solution and next to this a sterile beaker on its side with a sterile filter paper in it. Use sterile forceps to aseptically remove glumes from the first seed. Immerse this seed in the 50% sodium hypochlorite. Remove glumes from a second seed and immerse the second seed into the sodium hypochlorite solution whilst removing the first seed and storing this dehusked/sterilized seed on the filter paper in the beaker. Continue.
After all the glumes are removed:
Sterilize dehusked seeds: 50% sodium hypochlorite: 5 min. with agitation.
Rinse: 5-7× in sterile deionized water, drain.
Place all seeds in a large sterile Petri dish. Aliquot for embryo excision (to keep seeds from drying out, work with only 50-100 in the plate at a time leaving the rest in the master plate).
Remove the embryo from each seed and place embryo, scutellum up, in a 90×15 mm Petri dish containing proliferation medium (40-50 embryos/plate). Culture at 28° C. in the dark for 2 days prior to bombardment
Day 3:
Check each Embryo for Contamination before Blasting
Remove the embryos from the proliferation medium. Distribute 35-40 embryos scutellum upwards in an area 1 cm2 in the centre of a 60×15 mm target plate containing 10 ml of proliferation medium+osmoticum (0.6 M). Check each target plate so that the scutellum is straight. Allow enough room so the scutella do not shade each other out.
Bombardment:
















Gun
14 kV




Vacuum: 25 inches of Hg



1st bombardment
4 hours after osmoticum treatment



2nd bombardment
4 hours after 1st bombardment










Day 4:

4-16 hours after the 2nd blast transfer immature embryos to proliferation medium without osmoticum. Culture in the dark at 28° C. for 2 days.
Selection:
Day 5:
Aseptically cut out with scissors the germinating shoot. Transfer 16-20 immature embryos to fresh proliferation medium containing 30-50 mg/l Hygromycin (depending on the genotype); culture in the dark at 28° C.; record total number of embryos.
After 10 days carefully remove the callus from the scutellum by breaking it up into 2-10 small pieces; subculture onto fresh proliferation medium+hygromycin. Do not subculture brown tissue and remaining immature embryo which could inhibit further growth of healthy callus.
Subculture every 10 days by selecting healthy tissue: (embryogenic if present) and transfer it to fresh proliferation medium+hygromycin. Remove brown callus as it could be inhibiting to Embryogenic callus.
30 to 40 days after bombardment change selection procedure. Instead of eliminating bad-looking tissue keep embryogenic tissue only (eliminate healthy non-embryogenic tissue)
Regeneration:
After 40 to 60 days, transfer established embryogenic callus showing differential growth on proliferation medium+hygromycin to regeneration medium+hygromycin. Culture at 28° C. under low light for 10 days then under high light for 10 additional days. Check plates periodically in the light for the development of embryos and green shoots. As shoots develop it is sometimes beneficial to gently move the developing shoot away from the callus it originated from and remove any dead tissue from the shoot itself to prevent inhibition of growth.
Germination:
Transfer white compact embryos and green shoots initiating roots to the germination medium under high light at 28° C. for 1 to 2 weeks. Check plates periodically. Remove necrotic tissue and divide germinating embryos if necessary.
Results
The transformation of Nicotiana tabacum and rice was performed with group II intron-based vectors containing transgene cassettes for transformation of the mitochondrial genome.
Seven to ten independent transgenic lines were analysed for each construct. Molecular analyses including sequencing of insert junctions showed that there was correct insertion in the mitochondrial genome in 80% of transformed plants. Insertion of the PCF open reading frame in the plant mitochondria was correlated with a sterility phenotype.
The analysis of transgenic plants was performed using PCR for insertion flanking sequences using the following pairs, of primers:
For Tobacco:











ntLFS3F
cccaagttacagcgggctct
SEQ ID NO. 66



 



PCFMR
tatggggcttccctgtcgag
SEQ ID NO. 67



 



PCFMF
gcagcaccaaaattgagcct
SEQ ID NO. 68



 



ntRFS3R
cgagttccagaggcatcttc
SEQ ID NO. 69






For Rice:










osLFSF
actgaatgcggaaagtatgg
SEQ ID NO. 70


 


PCFMR
tatggggcttccctgtcgag
SEQ ID NO. 71


 


PCFMF
gcagcaccaaaattgagcct
SEQ ID NO. 72


 


osRFSR
tagggctactagaaagagga
SEQ ID NO. 73

## Claims

1. A method of transforming a plant cell, the method comprising:
1) introducing into the plant cell a first nucleic acid sequence that comprises a plant nuclear promoter operably linked to a first nucleic acid sequence that comprises a plant mitochondrion transgene cassette, a plant mitochondrion translocation sequence from a group II intron RNA, wherein the group II intron is Ll.LtrB, and a primer binding domain; and
2) introducing into the plant cell a second nucleic acid sequence that encodes for a translocation sequence binding protein from an intron encoded protein (IEP) of a group II intron,
wherein the IEP is LtrA fused to a plant mitochondrion transit peptide,
wherein the second nucleic acid sequence is operably linked to a plant nuclear promoter, and
wherein the mitochondrion translocation sequence of the product of 1) binds with the translocation sequence binding protein of the product of 2).

2. The method according to claim 1, wherein the plant mitochondrion transgene cassette comprises:
i) a left flanking sequence (LFS) having least one mitochondrion specific promoter (mPRO) and a right flanking sequence (RFS) having at least one mitochondrion specific terminator (mTER) sequence; and
ii) at least one isolated nucleic acid of interest.

3. The method according to claim 1, wherein the said isolated nucleic acid sequence is a recombinant DNA sequence or an introduced native, isolated genomic DNA sequence selected from isolated mammalian or plant nucleic acid sequences.

4. The method according to claim 3, wherein the isolated nucleic acid sequence is selected from nucleic acid sequences encoding proteins that confer cytoplasmic male sterility to a plant.

5. The method according to claim 1, wherein the primer binding domain is selected from that of a retrotransposon, or of a retrovirus.

6. A method of producing at least a heterologous or exogenous RNA species in a plant that comprises:
1) introducing into a regenerable plant cell a nucleic acid sequence that comprises a plant nuclear promoter operably linked to a first nucleic acid sequence that comprises a plant mitochondrion transgene cassette, a plant mitochondrion translocation sequence from a group II intron RNA, wherein the group II intron is Ll.LtrB, and a primer binding domain;
2) introducing into the regenerable plant cell a second nucleic acid sequence that encodes for a translocation sequence binding protein from an intron encoded protein (IEP) of a group II intron, wherein the IEP is LtrA fused to a plant mitochondrion transit peptide, and wherein said second nucleic acid sequence is operably linked to a plant nuclear promoter;
3) growing the regenerable plant cell of steps 1) to 2);
4) selecting a plant cell of 3), wherein the transgene comprised within the plant mitochondrion transgene cassette is integrated into the mitochondrial genome;
5) regenerating a plant from the plant cell of 4); and
6) growing the plant of 5).

7. The method according to claim 6, wherein the heterologous or exogenous RNA species encoded by the transgene that is integrated into the mitochondrion is expressed as a heterologous or exogenous protein.

8. An isolated polynucleotide sequence that comprises a plant nuclear promoter operably linked to a first nucleic acid sequence that comprises a plant mitochondrion transgene cassette, a plant mitochondrion translocation sequence from a group II intron RNA, wherein the group II intron is Ll.LtrB, and a primer binding domain for use in a method according to claim 1.

9. An isolated polynucleotide sequence that encodes for a mitochondrion translocation sequence-binding protein fused to a plant mitochondrion transit peptide wherein the polynucleotide sequence is operably linked to a plant nuclear promoter for use in a method according to claim 1.

10. An isolated polynucleotide sequence that encodes for a mitochondrion translocation sequence-binding protein from an intron encoded protein (IEP) of a group II intron, wherein the IEP is LtrA fused to a plant mitochondrion transit peptide, and wherein the polynucleotide sequence is operably linked to a plant nuclear promoter for use in a method according to claim 6.

11. An isolated polynucleotide sequence that encodes for a reverse transcriptase protein fused to a plant mitochondrion transit peptide, wherein the polynucleotide sequence is operably linked to a plant nuclear promoter for use in a method according to claim 1.

12. An isolated polynucleotide sequence that encodes for a reverse transcriptase protein fused to a plant mitochondrion transit peptide wherein the polynucleotide sequence is operably linked to a plant nuclear promoter for use in a method according to claim 6.

13. The isolated polynucleotide sequence according to claim 8 comprising genomic DNA or cDNA.

14. A cell containing a heterologous polynucleotide according to claim 8 comprised in a plant, a plant part, or a plant propagule, or in plant cell culture wherein the plant is selected from the group consisting of tobacco (Nicotiana tabacum) and other Nicotiana species, carrot, vegetable and oilseed Brassicas, melons, capsicums, grape vines, lettuce, strawberry, sugar beet, wheat, barley, corn (maize), rice, peas, sorghum, sunflower, tomato, cotton, and potato.

15. The method according to claim 3, wherein the isolated nucleic acid sequence is selected from nucleic acid sequences encoding proteins selected from the petunia mitochondrion pcf sequence, the orf107 sequence of sorghum and the orf79 of rice.

16. The method according to claim 1, wherein the primer binding domain is selected from the yeast Ty1 retrotransposon and the TnT1 tobacco retrotransposon.

17. The method according to claim 1, wherein the MTS sequence is selected from the group II intron-derived MTS from the Lactococcus lactis Ll.LtrB intron.