The Plant Journal

Hu, Yuxin; Poh, Huay Mei; Chua, Nam‐Hai

doi: 10.1111/j.1365-313X.2006.02750.xpmid: 16824178

Cell expansion, and its coordination with cell division, plays a critical role in the growth and development of plant organs. However, the genes controlling cell expansion during organogenesis are largely unknown. Here, we demonstrate that a novel Arabidopsis gene, ARGOS‐LIKE (ARL), which has some sequence homology to the ARGOS gene, is involved in this process. Reduced expression or overexpression of ARL in Arabidopsis results in smaller or larger cotyledons and leaves as well as other lateral organs, respectively. Anatomical examination of cotyledons and leaves in ARL transgenic plants demonstrates that the alteration in size can be attributed to changes in cell size rather than cell number, indicating that ARL plays a role in cell expansion‐dependent organ growth. ARL is upregulated by brassinosteroid (BR) and this induction is impaired in the BR‐insensitive mutant bri1, but not in the BR‐deficient mutant det2. Ectopic expression of ARL in bri1–119 partially restores cell growth in cotyledons and leaves. Our results suggest that ARL acts downstream of BRI1 and partially mediates BR‐related cell expansion signals during organ growth.

Skirycz, Aleksandra; Reichelt, Michael; Burow, Meike; Birkemeyer, Claudia; Rolcik, Jakub; Kopka, Joachim; Zanor, Maria Inès; Gershenzon, Jonathan; Strnad, Miroslav; Szopa, Jan; Mueller‐Roeber, Bernd; Witt, Isabell

Talmor‐Neiman, Mali; Stav, Ran; Frank, Wolfgang; Voss, Bjoern; Arazi, Tzahi

doi: 10.1111/j.1365-313X.2006.02768.xpmid: 16824179

Micro‐RNAs (miRNAs) are one class of small non‐coding RNAs that have important regulatory roles in higher plants. Much less is known about their prevalence and function in lower land plants. Previously we cloned 100 non‐structural small RNAs from the moss Physcomitrella patens but could annotate only 11 as miRNAs. To identify additional moss miRNAs among cloned small RNAs we have analyzed their genomic sequences for a characteristic miRNA precursor‐like structure. This analysis revealed 19 new moss miRNAs that are predicted to be encoded by 22 putative foldbacks. Northern blot analysis confirmed the expression of 14 new miRNA representatives. Half of these were gametophore specific, the rest were detected at low levels in the protonema. We predicted 12 genes as targets of nine new miRNAs. Three of these show homology to transcription factors and the others appear to play roles in diverse physiological processes including light and cytokine signaling, which have not to date been shown to be regulated by a miRNA in flowering plants. Four target genes, which show homology to ATN1‐like protein kinase, NAC transcription factors and a cytokinin receptor, have been validated by miRNA‐mediated mRNA cleavage. In addition, our analysis revealed that seven small RNAs represent miRNA* and three represent intermediates of pre‐miRNA processing, providing evidence for specific DICER‐like cleavage steps during miRNA biogenesis in moss. Our findings suggest that miRNAs are common in mosses and set the stage for the elucidation of their varied biological functions.

Kuang, Hanhui; Ochoa, Oswaldo E.; Nevo, Eviatar; Michelmore, Richard W.

doi: 10.1111/j.1365-313X.2006.02755.xpmid: 16762035

Resistance genes can exhibit heterogeneous patterns of variation. However, there are few data on their frequency and variation in natural populations. We analysed the frequency and variation of the resistance gene Dm3, which confers resistance to Bremia lactucae (downy mildew) in 1033 accessions of Lactuca serriola (prickly lettuce) from 49 natural populations. Inoculations with an isolate of Bremia lactucae carrying avirulence gene Avr3 indicated that the frequency of Dm3 in natural populations of L. serriola was very low. Molecular analysis demonstrated that Dm3 was present in only one of the 1033 wild accessions analysed. The sequence of the 5′ region of Dm3 was either highly conserved among accessions, or absent. In contrast, frequent chimeras were detected in the 3′ leucine‐rich repeat‐encoding region. Therefore low frequency of the Dm3 specificity in natural populations was due to either the recent evolution of Dm3 specificity, or deletions of the whole gene as well as variation in 3′ region caused by frequent gene conversions. This is the most extensive analysis of the prevalence of a known disease resistance gene to date, and indicates that the total number of resistance genes in a species may be very high. This has implications for the scales of germplasm conservation and exploitation of sources of resistance.

Yoine, Masato; Ohto, Masa‐aki; Onai, Kiyoshi; Mita, Satoru; Nakamura, Kenzo

doi: 10.1111/j.1365-313X.2006.02771.xpmid: 16740149

The low‐beta‐amylase1 (lba1) mutant of Arabidopsis thaliana has reduced sugar‐induced expression of Atβ‐Amy and shows pleiotropic phenotypes such as early flowering; short day‐sensitive growth; and seed germination that is hypersensitive to glucose and abscisic acid and resistant to mannose. lba1 was a missense mutation of UPF1 RNA helicase involved in nonsense‐mediated mRNA decay (NMD), which eliminates mRNAs with premature termination codons (PTCs), and replaces highly conserved Gly851 of UPF1 with Glu. Expression of the wild‐type UPF1 in lba1 rescued not only the reduced sugar‐inducible gene expression, but also early flowering and altered seed‐germination phenotypes. Sugar‐inducible mRNAs were over‐represented among transcripts decreased in sucrose‐treated lba1 compared with Col plants, suggesting that UPF1 is involved in the expression of a subset of sugar‐inducible genes. On the other hand, transcripts increased in lba1, which are likely to contain direct targets of NMD, included mRNAs for many transcription factors and metabolic enzymes that play diverse functions. Among these, the level of an alternatively spliced transcript of AtTFIIIA containing PTC was 17‐fold higher in lba1 compared with Col plants, and it was reduced to the level in Col by expressing the wild‐type UPF1. The lba1 mutant provides a good tool for studying NMD in plants.

Ziolkowski, Piotr A.; Kaczmarek, Malgorzata; Babula, Danuta; Sadowski, Jan

doi: 10.1111/j.1365-313X.2006.02762.xpmid: 16824180

Since the tetraploidization of the Arabidopsis thaliana ancestor 30–35 million years ago (Mya), a wave of chromosomal rearrangements have modified its genome architecture. The dynamics of this process is unknown, as it has so far been impossible to date individual rearrangement events. In this paper, we present evidence demonstrating that the majority of rearrangements occurred before the Arabidopsis–Brassica split 20–24 Mya, and that the segmental architecture of the A. thaliana genome is predominantly conserved in Brassica. This finding is based on the conservation of four rearrangement breakpoints analysed by fluorescence in situ hybridization (FISH) and RFLP mapping of three A. thaliana chromosomal regions. For this purpose, 95 Arabidopsis bacterial artificial chromosomes (BACs) spanning a total of 8.25 Mb and 81 genetic loci for 36 marker genes were studied in the Brassica oleracea genome. All the regions under study were triplicated in the B. oleracea genome, confirming the hypothesis of Brassica ancestral genome triplication. However, whilst one of the breakpoints was conserved at one locus, it was not at the two others. Further comparison of their organization may indicate that the evolution of the hexaploid Brassica progenitor proceeded by several events, separated in time. Genetic mapping and reprobing with rDNA allowed assignment of the regions to particular Brassica chromosomes. Based on this study of regional organization and evolution, a new insight into polyploidization/diploidization cycles is proposed.

Tang, Dingzhong; Ade, Jules; Frye, Catherine A.; Innes, Roger W.

doi: 10.1111/j.1365-313X.2006.02769.xpmid: 16824181

We screened for mutants of Arabidopsis thaliana that displayed enhanced disease resistance to the powdery mildew pathogen Erysiphe cichoracearum and identified the edr3 mutant, which formed large gray lesions upon infection with E. cichoracearum and supported very little sporulation. The edr3‐mediated disease resistance and cell death phenotypes were dependent on salicylic acid signaling, but independent of ethylene and jasmonic acid signaling. In addition, edr3 plants displayed enhanced susceptibility to the necrotrophic fungal pathogen Botrytis cinerea, but showed normal responses to virulent and avirulent strains of Pseudomonas syringae pv. tomato. The EDR3 gene was isolated by positional cloning and found to encode Arabidopsis dynamin‐related protein 1E (DRP1E). The edr3 mutation caused an amino acid substitution in the GTPase domain of DRP1E (proline 77 to leucine) that is predicted to block GTP hydrolysis, but not GTP binding. A T‐DNA insertion allele in DRP1E did not cause powdery mildew‐induced lesions, suggesting that this phenotype is caused by DRP1E being locked in the GTP‐bound state, rather than by a loss of DRP1E activity. Analysis of DRP1E–green fluorescent protein fusion proteins revealed that DRP1E is at least partially localized to mitochondria. These observations suggest a mechanistic link between salicylic acid signaling, mitochondria and programmed cell death in plants.

Yahiaoui, Nabila; Brunner, Susanne; Keller, Beat

doi: 10.1111/j.1365-313X.2006.02772.xpmid: 16740148

Plant defence against pathogens is controlled by disease resistance (R) gene products that directly or indirectly detect specific pathogen effectors. Plant–pathogen interactions have been proposed to follow a co‐evolutionary arms‐race model where R genes are recent and evolve rapidly in response to structural changes in matching pathogen effectors. However, the longevity and extensive polymorphism of R genes studied were more consistent with balancing selection maintaining ancient and diverse R genes or alleles. In bread wheat (Triticum aestivum), the Pm3 locus confers race‐specific resistance to wheat powdery mildew (Blumeria graminis f.sp. triticii). Here we describe recently generated Pm3 resistance alleles that all derive from one susceptible allele, Pm3CS, which is widespread among hexaploid bread‐wheat lines. One group of four Pm3 resistance alleles shows few, clearly delimited, polymorphic sequence blocks of ancient origin, embedded in sequences identical to Pm3CS and possibly derived from gene conversion. A second group of three alleles differs from Pm3CS by only two to five mutations, all non‐synonymous, and all in the leucine‐rich repeat‐encoding region. Transient transformation experiments confirmed that Pm3 resistance specificities are based on one or few amino acid changes. The Pm3CS allele was found in wild tetraploid wheat, the ancestor of hexaploid bread wheat, specifically from southern Turkey, a region proposed to be the site of wheat domestication. Based on these data, we propose that the Pm3 resistance alleles were generated in agricultural ecosystems after domestication of wheat 10 000 years ago. The evolution of Pm3 alleles in wheat is best described by the model of evolved recycling, where novel genetic variation is integrated in plant populations together with recycling of old variation.

Kuusk, Sandra; Sohlberg, Joel J.; Magnus Eklund, D.; Sundberg, Eva

doi: 10.1111/j.1365-313X.2006.02774.xpmid: 16740146

Gene duplication events, and the subsequent functional divergence of duplicates, are believed to be important evolutionary agents, driving morphological diversification. We have studied the structural and functional diversification of members of a plant‐specific gene family in Arabidopsis thaliana by analysing mutant phenotypes, expression patterns and phylogeny. The SHI gene family comprises ten members that encode proteins with a RING finger‐like zinc finger motif. We show that, despite being highly divergent in sequence, except in two conserved regions, many of the SHI‐related genes are partially redundant in function and synergistically promote gynoecium, stamen and leaf development in Arabidopsis. Gynoecia of the loss‐of‐function sty1‐1 mutant display subtle morphological defects, and, although mutations in the related STY2, SHI, SRS3, SRS4, SRS5, SRS7 and LRP1 genes have no apparent effect on gynoecium development, the sty1‐1 mutant phenotype is gradually enhanced in double, triple, quadruple and quintuple mutant combinations, suggesting a remarkably extensive functional conservation within the family, which appears to be based on dosage dependency and protection against dominant negative mutations. In multiple mutant lines, all marginal tissues in the apical part of the gynoecium are dramatically reduced or missing, and our data indicate that SHI family members may promote formation of these tissues downstream of the transcriptional co‐repressor LEUNIG (LUG).

Sohlberg, Joel J.; Myrenås, Mattias; Kuusk, Sandra; Lagercrantz, Ulf; Kowalczyk, Mariusz; Sandberg, Göran; Sundberg, Eva

doi: 10.1111/j.1365-313X.2006.02775.xpmid: 16740145

Gynoecia of the Arabidopsis mutant sty1‐1 display abnormal style morphology and altered vascular patterning. These phenotypes, which are enhanced in the sty1‐1 sty2‐1 double mutant, suggest that auxin homeostasis or signalling might be affected by mutations in STY1 and STY2, both members of the SHI gene family. Chemical inhibition of polar auxin transport (PAT) severely affects the apical–basal patterning of the gynoecium, as do mutations in the auxin transport/signalling genes PIN1, PID and ETT. Here we show that the apical–basal patterning of sty1‐1 and sty1‐1 sty2‐1 gynoecia is hypersensitive to reductions in PAT, and that sty1‐1 enhances the PAT inhibition‐like phenotypes of pin1‐5, pid‐8 and ett‐1 gynoecia. Furthermore, we show that STY1 activates transcription of the flavin monooxygenase‐encoding gene THREAD/YUCCA4, involved in auxin biosynthesis, and that changes in expression of STY1 and related genes lead to altered auxin homeostasis. Our results suggest that STY1 and related genes promote normal development of the style and affect apical–basal patterning of the gynoecium through regulation of auxin homeostasis.