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Veremeichik GN, Bulgakov DV, Solomatina TO, Makhazen DS. In the interkingdom horizontal gene transfer, the small rolA gene is a big mystery. Appl Microbiol Biotechnol 2023; 107:2097-2109. [PMID: 36881118 DOI: 10.1007/s00253-023-12454-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023]
Abstract
The biological function of the agrobacterial oncogene rolA is very poorly understood compared to other components of the mechanism of horizontal gene transfer during agrobacterial colonization of plants. Research groups around the world have worked on this problem, and available information is reviewed in this review, but other rol oncogenes have been studied much more thoroughly. Having one unexplored element makes it impossible to form a complete picture. However, the limited data suggest that the rolA oncogene and its regulatory apparatus have great potential in plant biotechnology and genetic engineering. Here, we collect and discuss available experimental data about the function and structure of rolA. There is still no clear understanding of the mechanism of RolA and its structure and localization. We believe this is because of the nucleotide structure of a frameshift in the most well-studied rolA gene of the agropine type pRi. In fact, interest in the genes of agrobacteria as natural tools for the phenotypic or biochemical engineering of plants increased. We believe that a detailed understanding of the molecular mechanisms will be forthcoming. KEY POINTS: • Among pRi T-DNA oncogenes, rolA is the least understood in spite of many studies. • Frameshift may be the reason for the failure to elucidate the role of agropine rolA. • Understanding of rolA is promising for the phenotypic and biochemical engineering of plants.
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Affiliation(s)
- Galina N Veremeichik
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Russian Academy of Sciences Far Eastern Branch, FGBUN FNC Bioraznoobrazia nazemnoj bioty Vostocnoj Azii Dal'nevostocnogo otdelenia Rossijskoj akademii nauk, 690022, Vladivostok, Russia.
| | - Dmitrii V Bulgakov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Russian Academy of Sciences Far Eastern Branch, FGBUN FNC Bioraznoobrazia nazemnoj bioty Vostocnoj Azii Dal'nevostocnogo otdelenia Rossijskoj akademii nauk, 690022, Vladivostok, Russia
| | - Taisia O Solomatina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Russian Academy of Sciences Far Eastern Branch, FGBUN FNC Bioraznoobrazia nazemnoj bioty Vostocnoj Azii Dal'nevostocnogo otdelenia Rossijskoj akademii nauk, 690022, Vladivostok, Russia
| | - Dmitrii S Makhazen
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Russian Academy of Sciences Far Eastern Branch, FGBUN FNC Bioraznoobrazia nazemnoj bioty Vostocnoj Azii Dal'nevostocnogo otdelenia Rossijskoj akademii nauk, 690022, Vladivostok, Russia
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Veremeichik GN, Bulgakov VP, Shkryl YN, Silantieva SA, Makhazen DS, Tchernoded GK, Mischenko NP, Fedoreyev SA, Vasileva EA. Activation of anthraquinone biosynthesis in long-cultured callus culture of Rubia cordifolia transformed with the rolA plant oncogene. J Biotechnol 2019; 306:38-46. [PMID: 31526834 DOI: 10.1016/j.jbiotec.2019.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/11/2019] [Indexed: 01/06/2023]
Abstract
The RolA protein belongs to the RolB class of plant T-DNA oncogenes, and shares structural similarity with the papilloma virus E2 DNA-binding domain. It has potentially as an inducer of plant secondary metabolism, although its role in biotechnology has yet to be realised. In this investigation, a Rubia cordifolia callus culture transformed with the rolA plant oncogene for more than 10 years was analysed. Expression of the rolA gene in the callus line was stable during long-term cultivation, and growth parameters were both elevated and stable, exceeding those of the non-transformed control culture. The rolA-transformed calli not only demonstrated remarkably stable growth, but also the ability to increase the yield of anthraquinones (AQs) in long-term cultivation. After ten years of cultivating rolA callus lines, we observed an activation of AQ biosynthesis from 200 mg/l to 874 mg/l. The increase was mainly due to activation of ruberitrinic acid biosynthesis. The expression of key AQ biosynthesis genes was strongly activated in rolA-transgenic calli. We compared the effects of the rolA gene with those of the rolB gene, which was previously considered the most potent inducer of secondary metabolism, and showed that rolA was more productive under conditions of long-term cultivation.
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Affiliation(s)
- G N Veremeichik
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia.
| | - V P Bulgakov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia; Far Eastern Federal University, Vladivostok, 690950, Russia
| | - Y N Shkryl
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - S A Silantieva
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - D S Makhazen
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - G K Tchernoded
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - N P Mischenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - S A Fedoreyev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - E A Vasileva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
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Modulation of endogenous indole-3-acetic acid biosynthesis in bacteroids within Medicago sativa nodules. Appl Environ Microbiol 2014; 80:4286-93. [PMID: 24814784 DOI: 10.1128/aem.00597-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To evaluate the dose-response effects of endogenous indole-3-acetic acid (IAA) on Medicago plant growth and dry weight production, we increased the synthesis of IAA in both free-living and symbiosis-stage rhizobial bacteroids during Rhizobium-legume symbiosis. For this purpose, site-directed mutagenesis was applied to modify an 85-bp promoter sequence, driving the expression of iaaM and tms2 genes for IAA biosynthesis. A positive correlation was found between the higher expression of IAA biosynthetic genes in free-living bacteria and the increased production of IAA under both free-living and symbiotic conditions. Plants nodulated by RD65 and RD66 strains, synthetizing the highest IAA concentration, showed a significant (up to 73%) increase in the shoot fresh weight and upregulation of nitrogenase gene, nifH, compared to plants nodulated by the wild-type strain. When these plants were analyzed by confocal microscopy, using an anti-IAA antibody, the strongest signal was observed in bacteroids of Medicago sativa RD66 (Ms-RD66) plants, even when they were located in the senescent nodule zone. We show here a simple system to modulate endogenous IAA biosynthesis in bacteria nodulating legumes suitable to investigate which is the maximum level of IAA biosynthesis, resulting in the maximal increase of plant growth.
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Catania F, Gao X, Scofield DG. Endogenous mechanisms for the origins of spliceosomal introns. J Hered 2009; 100:591-6. [PMID: 19635762 DOI: 10.1093/jhered/esp062] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Over 30 years since their discovery, the origin of spliceosomal introns remains uncertain. One nearly universally accepted hypothesis maintains that spliceosomal introns originated from self-splicing group-II introns that invaded the uninterrupted genes of the last eukaryotic common ancestor (LECA) and proliferated by "insertion" events. Although this is a possible explanation for the original presence of introns and splicing machinery, the emphasis on a high number of insertion events in the genome of the LECA neglects a considerable body of empirical evidence showing that spliceosomal introns can simply arise from coding or, more generally, nonintronic sequences within genes. After presenting a concise overview of some of the most common hypotheses and mechanisms for intron origin, we propose two further hypotheses that are broadly based on central cellular processes: 1) internal gene duplication and 2) the response to aberrant and fortuitously spliced transcripts. These two nonmutually exclusive hypotheses provide a powerful way to explain the establishment of spliceosomal introns in eukaryotes without invoking an exogenous source.
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Affiliation(s)
- Francesco Catania
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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Introduction of a novel pathway for IAA biosynthesis to rhizobia alters vetch root nodule development. Arch Microbiol 2008; 190:67-77. [DOI: 10.1007/s00203-008-0365-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Revised: 01/22/2008] [Accepted: 03/17/2008] [Indexed: 10/22/2022]
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Xue ZT, Holefors A, Welander M. Intron splicing in 5' untranslated region of the rolA transcript in transgenic apple. JOURNAL OF PLANT PHYSIOLOGY 2008; 165:544-52. [PMID: 17490782 DOI: 10.1016/j.jplph.2006.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 11/21/2006] [Accepted: 11/24/2006] [Indexed: 05/15/2023]
Abstract
The rolA gene encoded on the Ri plasmid of Agrobacterium rhizogenes causes developmental alterations, including dwarfing characteristics in the transgenic plants. In an attempt to introduce dwarfing characteristics into apple rootstocks for breeding purposes, the rolA gene was incorporated into the apple rootstock M26 and obtained four transgenic clones. All the clones exhibited reduced growth compared to untransformed control plants but different degree of dwarfing and wrinkled leaves. In the present study, expression of the rolA gene was further investigated by analysing the structure of the rolA transcript and the levels of the rolA mRNAs from these clones. The nucleotide (nt) sequence of the rolA transcript showed two forms of the transcript: one, the unspliced form, was co-linear with the rolA sequence in the genomic DNA; the other was spliced mRNA in which an 85-base pair (bp) intron sequence in the 5' untranslated region (5'UTR) was spliced out. The position of splicing is different from that in Arabidopsis thaliana but similar to the splicing site found in tobacco. The transcription start region of the rolA gene in apple was 206bp upstream of that in Arabidopsis and 277bp upstream to Nicotiana tabacum transcription start. A hairpin-like secondary structure and an upstream open reading frame (uORF) were revealed in the rolA 5'UTR. The levels of the rolA mRNA in the apple transgenic clones were analysed by semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR). The results showed slight variation in the shoot tissues of the transgenic clones.
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Affiliation(s)
- Zhong-Tian Xue
- Department of Crop Science, The Swedish University of Agricultural Sciences, PO Box 55, S-230 53 Alnarp, Sweden
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Pii Y, Crimi M, Cremonese G, Spena A, Pandolfini T. Auxin and nitric oxide control indeterminate nodule formation. BMC PLANT BIOLOGY 2007; 7:21. [PMID: 17488509 PMCID: PMC1878477 DOI: 10.1186/1471-2229-7-21] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Accepted: 05/08/2007] [Indexed: 05/15/2023]
Abstract
BACKGROUND Rhizobia symbionts elicit root nodule formation in leguminous plants. Nodule development requires local accumulation of auxin. Both plants and rhizobia synthesise auxin. We have addressed the effects of bacterial auxin (IAA) on nodulation by using Sinorhizobium meliloti and Rhizobium leguminosarum bacteria genetically engineered for increased auxin synthesis. RESULTS IAA-overproducing S. meliloti increased nodulation in Medicago species, whilst the increased auxin synthesis of R. leguminosarum had no effect on nodulation in Phaseolus vulgaris, a legume bearing determinate nodules. Indeterminate legumes (Medicago species) bearing IAA-overproducing nodules showed an enhanced lateral root development, a process known to be regulated by both IAA and nitric oxide (NO). Higher NO levels were detected in indeterminate nodules of Medicago plants formed by the IAA-overproducing rhizobia. The specific NO scavenger cPTIO markedly reduced nodulation induced by wild type and IAA-overproducing strains. CONCLUSION The data hereby presented demonstrate that auxin synthesised by rhizobia and nitric oxide positively affect indeterminate nodule formation and, together with the observation of increased expression of an auxin efflux carrier in roots bearing nodules with higher IAA and NO content, support a model of nodule formation that involves auxin transport regulation and NO synthesis.
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Affiliation(s)
- Youry Pii
- Dipartimento Scientifico Tecnologico, University of Verona, Verona, Italy
| | - Massimo Crimi
- Dipartimento Scientifico Tecnologico, University of Verona, Verona, Italy
| | - Giorgia Cremonese
- Dipartimento Scientifico Tecnologico, University of Verona, Verona, Italy
| | - Angelo Spena
- Dipartimento Scientifico Tecnologico, University of Verona, Verona, Italy
| | - Tiziana Pandolfini
- Dipartimento Scientifico Tecnologico, University of Verona, Verona, Italy
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Gorguet B, van Heusden AW, Lindhout P. Parthenocarpic fruit development in tomato. PLANT BIOLOGY (STUTTGART, GERMANY) 2005; 7:131-9. [PMID: 15822008 DOI: 10.1055/s-2005-837494] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Parthenocarpic fruit development is a very attractive trait for growers and consumers. In tomato, three main sources of facultative parthenocarpy, pat, pat-2, pat-3/pat-4, are known to have potential applications in agriculture. The parthenocarpic fruit development in these lines is triggered by a deregulation of the hormonal balance in some specific tissues. Auxins and gibberellins are considered as the key elements in parthenocarpic fruit development of those lines. An increased level of these hormones in the ovary can substitute for pollination and trigger fruit development. This has opened up genetic engineering approaches for parthenocarpy that have given promising results, both in quality and quantity of seedless fruit production.
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Affiliation(s)
- B Gorguet
- Laboratory of Plant Breeding, Graduate School of Plant Sciences, Wageningen University, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.
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Pandolfini T, Molesini B, Avesani L, Spena A, Polverari A. Expression of self-complementary hairpin RNA under the control of the rolC promoter confers systemic disease resistance to plum pox virus without preventing local infection. BMC Biotechnol 2003; 3:7. [PMID: 12823862 PMCID: PMC194883 DOI: 10.1186/1472-6750-3-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2003] [Accepted: 06/25/2003] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Homology-dependent selective degradation of RNA, or post-transcriptional gene silencing (PTGS), is involved in several biological phenomena, including adaptative defense mechanisms against plant viruses. Small interfering RNAs mediate the selective degradation of target RNA by guiding a multicomponent RNAse. Expression of self-complementary hairpin RNAs within two complementary regions separated by an intron elicits PTGS with high efficiency. Plum pox virus (PPV) is the etiological agent of sharka disease in Drupaceae, although it can also be transmitted to herbaceous species (e.g. Nicotiana benthamiana). Once inside the plant, PPV is transmitted via plasmodesmata from cell to cell, and at longer distances, via phloem. The rolC promoter drives expression in phloem cells. RolC expression is absent in both epidermal and mesophyll cells. The aim of the present study was to confer systemic disease resistance without preventing local viral infection. RESULTS In the ihprolC-PP197 gene (intron hair pin rolC PPV 197), a 197 bp sequence homologous to the PPV RNA genome (from base 134 to 330) was placed as two inverted repeats separated by the DNA sequence of the rolA intron. This hairpin construct is under the control of the rolC promoter.N. benthamiana plants transgenic for the ihprolC-PP197 gene contain siRNAs homologous to the 197 bp sequence. The transgenic progeny of ihprolC-PP197 plants are resistant to PPV systemic infection. Local infection is unaffected. Most (80%) transgenic plants are virus free and symptomless. Some plants (20%) contain virus in uninoculated apical leaves; however they show only mild symptoms of leaf mottling. PPV systemic resistance cosegregates with the ihprolC-PP197 transgene and was observed in progeny plants of all independent transgenic lines analyzed. SiRNAs of 23-25 nt homologous to the PPV sequence used in the ihprolC-PP197 construct were detected in transgenic plants before and after inoculation. Transitivity of siRNAs was observed in transgenic plants 6 weeks after viral inoculation. CONCLUSIONS The ihprolC-PP197 transgene confers systemic resistance to PPV disease in N. benthamiana. Local infection is unaffected. This transgene and/or similar constructs could be used to confer PPV resistance to fruit trees where systemic disease causes economic damage.
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Affiliation(s)
- Tiziana Pandolfini
- Dipartimento Scientifico-Tecnologico, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Barbara Molesini
- Dipartimento Scientifico-Tecnologico, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Linda Avesani
- Dipartimento Scientifico-Tecnologico, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Angelo Spena
- Dipartimento Scientifico-Tecnologico, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Annalisa Polverari
- Dipartimento Scientifico-Tecnologico, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
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Zhi N, Ohashi N, Rikihisa Y. Activation of a p44 pseudogene in Anaplasma phagocytophila by bacterial RNA splicing: a novel mechanism for post-transcriptional regulation of a multigene family encoding immunodominant major outer membrane proteins. Mol Microbiol 2002; 46:135-45. [PMID: 12366837 DOI: 10.1046/j.1365-2958.2002.03143.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Immunodominant 44 kDa major outer membrane proteins of Anaplasma phagocytophila (human granulocytic ehrlichiosis agent) are encoded by the p44 multigene family. One of the paralogues, p44-18 is predominantly expressed by A. phagocytophila in mammalian hosts, but is downregulated in the arthropod vector. The expression of p44-18 was upregulated in A. phagocytophila cultivated in HL-60 cells at 37 degrees C compared with 24 degrees C. However, the molecular mechanism of such gene expression was unclear, as p44-18 has a pseudogene-like structure, i.e. it lacks an AUG start codon and is out of frame with an upstream overlapping paralogue, p44-1. In the present study, we found that an amplicon detected by reverse transciption-polymerase chain reaction (RT-PCR) [808 basepair (bp)] for the p44-1/p44-18 gene locus was smaller than that detected by PCR with the genomic DNA (1652 bp) in the A. phagocytophila-infected HL-60 cells cultured at 37 degrees C. A circularized RNA molecule corresponding to the 844 bp region missing from the locus in the RT-PCR product was detected by inverse RT-PCR, indicating that this is an intron (designated p44-1 intervening sequence, p44-1 IVS). The splicing event of p44-1 IVS was also observed when the p44-1 IVS-carrying plasmid was introduced into Escherichia coli, suggesting that the splicing is sequence-dependent. Structural analysis and in vitro splicing experiments of p44-1 IVS suggested that this is likely to represent a new class of introns in eubacteria. The primer extension analysis showed the presence of a putative sigma(32)-type promoter in region upstream from p44-1. Collectively, the novel RNA splicing and the temperature-dependent transcription may account for the dominant p44-18 expression in mammals.
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Affiliation(s)
- Ning Zhi
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, 1925 Coffey Road, 43210-1093, USA
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Pandolfini T, Rotino GL, Camerini S, Defez R, Spena A. Optimisation of transgene action at the post-transcriptional level: high quality parthenocarpic fruits in industrial tomatoes. BMC Biotechnol 2002; 2:1. [PMID: 11818033 PMCID: PMC65046 DOI: 10.1186/1472-6750-2-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2001] [Accepted: 01/11/2002] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic engineering of parthenocarpy confers to horticultural plants the ability to produce fruits under environmental conditions that curtail fruit productivity and quality. The DefH9-iaaM transgene, whose predicted action is to confer auxin synthesis specifically in the placenta, ovules and derived tissues, has been shown to confer parthenocarpy to several plant species (tobacco, eggplant, tomato) and varieties. RESULTS UC82 tomato plants, a typical cultivar used by the processing industry, transgenic for the DefH9-iaaM gene produce parthenocarpic fruits that are malformed. UC82 plants transgenic for the DefH9-RI-iaaM, a DefH9-iaaM derivative gene modified in its 5'ULR by replacing 53 nucleotides immediately upstream of the AUG initiation codon with an 87 nucleotides-long sequence derived from the rolA intron sequence, produce parthenocarpic fruits of high quality. In an in vitro translation system, the iaaM mRNA, modified in its 5'ULR is translated 3-4 times less efficiently than the original transcript. An optimal expressivity of parthenocarpy correlates with a reduced transgene mRNA steady state level in DefH9-RI-iaaM flower buds in comparison to DefH9-iaaM flower buds. Consistent with the known function of the iaaM gene, flower buds transgenic for the DefH9-RI-iaaM gene contain ten times more IAA than control untransformed flower buds, but five times less than DefH9-iaaM flower buds. CONCLUSIONS By using an auxin biosynthesis transgene downregulated at the post-transcriptional level, an optimal expressivity of parthenocarpy has been achieved in a genetic background not suitable for the original transgene. Thus, the method allows the generation of a wider range of expressivity of the desired trait in transgenic plants.
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Affiliation(s)
- Tiziana Pandolfini
- Dipartimento Scientifico Tecnologico, University of Verona, Verona, Italy
| | - Giuseppe L Rotino
- Research Institute for Vegetable Crops, Montanaso Lombardo (LO), Italy
| | - Serena Camerini
- International Institute of Genetics and Biophysics, Naples, Italy
| | - Roberto Defez
- International Institute of Genetics and Biophysics, Naples, Italy
| | - Angelo Spena
- Dipartimento Scientifico Tecnologico, University of Verona, Verona, Italy
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Zhu J, Oger PM, Schrammeijer B, Hooykaas PJ, Farrand SK, Winans SC. The bases of crown gall tumorigenesis. J Bacteriol 2000; 182:3885-95. [PMID: 10869063 PMCID: PMC94570 DOI: 10.1128/jb.182.14.3885-3895.2000] [Citation(s) in RCA: 246] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- J Zhu
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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Pandolfini T, Storlazzi A, Calabria E, Defez R, Spena A. The spliceosomal intron of the rolA gene of agrobacterium rhizogenes is a prokaryotic promoter. Mol Microbiol 2000; 35:1326-34. [PMID: 10760134 DOI: 10.1046/j.1365-2958.2000.01810.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Agrobacterium rhizogenes transfers DNA (T-DNA) from its Ri plasmid to plant cells. All T-DNA genes are expressed in plant cells. The rolA gene is the only T-DNA gene that contains an intron in the untranslated leader region of its mRNA. This paper shows that (i) the rolA gene is also transcribed in bacteria; (ii) the 85 bp corresponding to the spliceosomal intron drives prokaryotic gene expression in agrobacteria, in free-living rhizobia and in bacteroids within root nodules; and (iii) promoter activity is abolished by the deletion of 63 bp from its 5' end and is reduced by mutations changing its sequence near the putative -10 region. The expression pattern of a chimeric reporter gene shows that, in free-living bacteria, gene expression takes place during the exponential phase of growth and increases at the onset of the stationary phase. Within root nodules, reporter gene expression occurs in the invasion, nitrogen fixing and senescent zones.
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Affiliation(s)
- T Pandolfini
- Faculty of Science, University of Verona, Verona, Italy
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Abstract
Xylanases are classified into two families, numbered F/10 and G/11 according to the similarity of amino acid sequences of their catalytic domain (Henrissat, B., Bairoch, A., 1993. New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 293, 781-788). Three-dimensional structure of the catalytic domain of the family F/10 xylanase was reported (White, A., Withers, S.G., Gilkes, N.R., Rose, D.R., 1994. Crystal structure of the catalytic domain of the beta-1,4-glycanase Cex from Cellulomonas fimi. Biochemistry 33, 12546-12552). The domain was decomposed into 22 modules by centripetal profiles (Go, M., Nosaka, M., 1987. Protein architecture and the origin of introns. Cold Spring Harbor Symp. Quant. Biol. 52, 915-924; Noguti, T., Sakakibara, H., Go, M., 1993. Localization of hydrogen-bonds within modules in barnase. Proteins 16, 357-363). A module is a contiguous polypeptide segment of amino acid residues having a compact conformation within a globular domain. Collected 31 intron sites of the family F/10 xylanase genes from fungus were found to be correlated to module boundaries with considerable statistical force (p values <0.001). The relationship between the intron locations and protein structures provides supporting evidence for the ancient origin of introns, because such a relationship cannot be expected by random insertion of introns into eukaryotic genes, but it rather suggests pre-existence of introns in the ancestral genes of prokaryotes and eukaryotes. A phylogenetic tree of the fungal and bacterial xylanase sequences made two clusters; one includes both the bacterial and fungal genes, but the other consists of only fungal genes. The mixed cluster of bacterial genes without introns and the fungal genes with introns further supports the ancient origin of introns. Comparison of the conserved base sequences of introns indicates that sliding of a splice site occurred in Aspergillus kawachii gene by one base from the ancestral position. Substrate-binding sites of xylanase are localized on eight modules, and introns are found at both termini of six out of these functional modules. This result suggests that introns might play a functional role in shuffling the exons encoding the substrate-binding modules.
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Affiliation(s)
- Y Sato
- Division of Biological Science, Graduate School of Science, Nagoya University, Japan
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Simpson GG, Filipowicz W. Splicing of precursors to mRNA in higher plants: mechanism, regulation and sub-nuclear organisation of the spliceosomal machinery. PLANT MOLECULAR BIOLOGY 1996; 32:1-41. [PMID: 8980472 DOI: 10.1007/bf00039375] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The removal of introns from pre-mRNA transcripts and the concomitant ligation of exons is known as pre-mRNA splicing. It is a fundamental aspect of constitutive eukaryotic gene expression and an important level at which gene expression is regulated. The process is governed by multiple cis-acting elements of limited sequence content and particular spatial constraints, and is executed by a dynamic ribonucleoprotein complex termed the spliceosome. The mechanism and regulation of pre-mRNA splicing, and the sub-nuclear organisation of the spliceosomal machinery in higher plants is reviewed here. Heterologous introns are often not processed in higher plants indicating that, although highly conserved, the process of pre-mRNA splicing in plants exhibits significant differences that distinguish it from splicing in yeast and mammals. A fundamental distinguishing feature is the presence of and requirement for AU or U-rich intron sequence in higher-plant pre-mRNA splicing. In this review we document the properties of higher-plant introns and trans-acting spliceosomal components and discuss the means by which these elements combine to determine the accuracy and efficiency of pre-mRNA processing. We also detail examples of how introns can effect regulated gene expression by affecting the nature and abundance of mRNA in plants and list the effects of environmental stresses on splicing. Spliceosomal components exhibit a distinct pattern of organisation in higher-plant nuclei. Effective probes that reveal this pattern have only recently become available, but the domains in which spliceosomal components concentrate were identified in plant nuclei as enigmatic structures some sixty years ago. The organisation of spliceosomal components in plant nuclei is reviewed and these recent observations are unified with previous cytochemical and ultrastructural studies of plant ribonuleoprotein domains.
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Affiliation(s)
- G G Simpson
- Friedrich Miescher-Institut, Basel, Switzerland
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17
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Natural genetic engineering of plant cells: the molecular biology of crown gall and hairy root disease. World J Microbiol Biotechnol 1996; 12:327-51. [DOI: 10.1007/bf00340209] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/07/1996] [Accepted: 02/10/1996] [Indexed: 11/26/2022]
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18
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Meyer AD, Ichikawa T, Meins F. Horizontal gene transfer: regulated expression of a tobacco homologue of the Agrobacterium rhizogenes rolC gene. MOLECULAR & GENERAL GENETICS : MGG 1995; 249:265-73. [PMID: 7500950 DOI: 10.1007/bf00290526] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A tobacco homologue (trolC) of the rolC gene of the Agrobacterium rhizogenes Ri-plasmid was cloned and sequenced from Nicotiana tabacum L. cv. Havana 425. The coding region of trolC is similar in sequence (69-87% for DNA and 54-89% for the deduced amino acid sequence) to rolC genes of the agropine, mannopine, and mikimopine strains of Ri-plasmids and the N. glauca rolC homologue. Southern analyses showed that trolC is encoded by a small gene family derived from the tomentosiformis ancestor of tobacco. This suggests that trolC resulted from an ancient transfer of DNA between A. rhizogenes and a progenitor of modern tobacco. Transcripts of trolC were detected in three morphologically distinct cultivars of tobacco. trolC mRNA accumulated in young leaves and shoot tips, but not in lower leaves and roots of mature plants. Accumulation of trolC mRNA in cultured leaf tissues was strongly down-regulated by auxin and induced by cytokinin. These results are of particular interest because they suggest that a gene of bacterial origin introduced during evolution can have a function in a modern plant.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Base Sequence
- Biological Evolution
- Blotting, Northern
- Blotting, Southern
- Cells, Cultured
- Cloning, Molecular
- Gene Expression Regulation, Plant
- Gene Transfer, Horizontal
- Genes, Plant
- Molecular Sequence Data
- Plant Proteins/genetics
- Plants, Toxic
- Rhizobium/genetics
- Sequence Alignment
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Nicotiana/cytology
- Nicotiana/genetics
- beta-Glucosidase
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Affiliation(s)
- A D Meyer
- Friedrich Miescher-Institute, Basel, Switzerland
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19
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Belfort M, Reaban ME, Coetzee T, Dalgaard JZ. Prokaryotic introns and inteins: a panoply of form and function. J Bacteriol 1995; 177:3897-903. [PMID: 7608058 PMCID: PMC177115 DOI: 10.1128/jb.177.14.3897-3903.1995] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- M Belfort
- Molecular Genetics Program, Wadsworth Center and School of Public Health, State University of New York at Albany 12201-2002, USA
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