Identification of BFN1, a bifunctional nuclease induced during leaf and stem senescence in Arabidopsis

Purification, properties and specificity of an endonuclease from Agropyron elongatum seedlings

An endonuclease was isolated from 5 days old Agropyron elongatum 8x = Elytrigia turcica McGuire seedlings. The enzyme was purified by means of ammonium sulfate fractionation, DEAE-cellulose and Heparin Sepharose column. The final preparation, named nuclease A, gave a single band after silver staining had followed SDS-electrophoresis that was identified with nuclease activities. The enzyme also showed a single band after activity staining on gel polymerized in the presence of heat denatured DNA (ssDNA)/RNA. The Mr of native enzyme was 36 and the enzyme's moiety consisted of one polypeptide chain. Nuclease A activity was stimulated in the presence of Zn(2+) and was moderately reduced by NaCl yet strongly by spermine. The enzyme had pH optimum 5.5 and isoelectric point (pI) 4.7. It hydrolyzed the nucleic acids in the order ssDNA > dsDNA > or = RNA; hence it was classified as a plant nuclease type I (EC 3.1.30.2). Synthetic homopolyribonucleotides were hydrolyzed in the order polyU > polyI > or = polyA > polyG > polyC. Nuclease A nicked the supercoiled plasmid DNA while it was incapable of hydrolyzing dinucleoside monophosphates. With regard to nuclease A base linkage specificity towards a synthetic 5'-(32)P labeled deoxydecanucleotide [5'-(32)P]CCTGGCAGTT, the enzyme firstly exhibited a preference to Ap downward arrow G bond and then to Gp downward arrow T, Cp downward arrow A and Gp downward arrow G bonds while it was incapable of hydrolyzing the Cp downward arrow C bond. The substrate's products of nuclease A were oligonucleotides with the monoesterified phosphate at the 3' position. Nuclease A may perform a crucial function in the metabolism of nucleic acids during seedling growth and could be used as a biochemical tool for analysis of nucleic acids structure.

Sugar-responsive gene expression, invertase activity, and senescence in aborting maize ovaries at low water potentials

BACKGROUND AND AIMS

Ovary abortion can occur in maize (Zea mays) if water deficits lower the water potential (psiw) sufficiently to inhibit photosynthesis around the time of pollination. The abortion decreases kernel number. The present work explored the activity of ovary acid invertases and their genes, together with other genes for sucrose-processing enzymes, when this kind of abortion occurred. Cytological evidence suggested that senescence may have been initiated after 2 or 3 d of low psiw, and the expression of some likely senescence genes was also determined.

METHODS

Ovary abortion was assessed at kernel maturity. Acid invertase activities were localized in vivo and in situ. Time courses for mRNA abundance were measured with real time PCR. Sucrose was fed to the stems to vary the sugar flux.

KEY RESULTS

Many kernels developed in controls but most aborted when psiw became low. Ovary invertase was active in controls but severely inhibited at low psiw for cell wall-bound forms in vivo and soluble forms in situ. All ovary genes for sucrose processing enzymes were rapidly down-regulated at low psiw except for a gene for invertase inhibitor peptide that appeared to be constitutively expressed. Some ovary genes for senescence were subsequently up-regulated (RIP2 and PLD1). In some genes, these regulatory changes were reversed by feeding sucrose to the stems. Abortion was partially prevented by feeding sucrose.

CONCLUSIONS

A general response to low psiw in maize ovaries was an early down-regulation of genes for sucrose processing enzymes followed by up-regulation of some genes involved in senescence. Because some of these genes were sucrose responsive, the partial prevention of abortion with sucrose feeding may have been caused in part by the differential sugar-responsiveness of these genes. The late up-regulation of senescence genes may have caused the irreversibility of abortion.

Mismatch cleavage by single-strand specific nucleases

We have investigated the ability of single-strand specific (sss) nucleases from different sources to cleave single base pair mismatches in heteroduplex DNA templates used for mutation and single-nucleotide polymorphism analysis. The TILLING (Targeting Induced Local Lesions IN Genomes) mismatch cleavage protocol was used with the LI-COR gel detection system to assay cleavage of amplified heteroduplexes derived from a variety of induced mutations and naturally occurring polymorphisms. We found that purified nucleases derived from celery (CEL I), mung bean sprouts and Aspergillus (S1) were able to specifically cleave nearly all single base pair mismatches tested. Optimal nicking of heteroduplexes for mismatch detection was achieved using higher pH, temperature and divalent cation conditions than are routinely used for digestion of single-stranded DNA. Surprisingly, crude plant extracts performed as well as the highly purified preparations for this application. These observations suggest that diverse members of the S1 family of sss nucleases act similarly in cleaving non-specifically at bulges in heteroduplexes, and single-base mismatches are the least accessible because they present the smallest single-stranded region for enzyme binding. We conclude that a variety of sss nucleases and extracts can be effectively used for high-throughput mutation and polymorphism discovery.

Arabidopsis whole-transcriptome profiling defines the features of coordinated regulations that occur during secondary growth

Secondary growth in the inflorescence stems of Arabidopsis plants was induced by a combination of short-day and long-day treatments. The induced stems were divided into three different stem developmental stages (i.e., immature, intermediate, and mature) with regard to secondary growth. Whole transcriptome microarrays were used to examine the changes in global gene expression occurring at the different stem developmental stages. Over 70% of the Arabidopsis transcriptome was expressed in the stem tissues. In the mature stems with secondary growth, 567 genes were upregulated 5-fold or higher and 530 were downregulated, when compared to immature stems (with no secondary growth) and 10-day old seedlings (with no inflorescence stem). The transcription phenotypes obtained from the stems at different developmental stages largely confirm the existing insights into the biochemical processes involved in the sequential events that lead to wood formation. The major difference found between the stems undergoing secondary growth and only primary growth was in the expression profiles of transcriptional regulation-and signal transduction-related genes. An analysis of several shoot apical meristem (SAM) activity-related gene expression patterns in the stems indicated that the genetic control of secondary meristem activity might be governed by a different mechanism from that of SAM. The current study established the expression patterns of many unknown genes and identified candidate genes that are involved in the genetic regulation of secondary growth. The findings described in this report should improve our understanding of the molecular mechanisms that regulate the growth and development of the stem.

RNase activity requires formation of disulfide bonds and is regulated by the redox state

The activity of many RNases requires the formation of one or more disulfide bonds which can contribute to their stability. In this study, we show that RNase activity and, to a much lesser extent, nuclease activity, are redox regulated. Intracellular RNase activity was altered in vitro by changes in the glutathione redox state. Moreover, RNase activity was abolished following exposure to reducing agents such as beta-ME or DTT. Following reduction with glutathione (GSH), RNase activity could be fully reactivated with oxidized glutathione (GSSG). In contrast, RNase activity could not be reactivated when reduced with DTT. Decreasing the level of glutathione in vivo in wheat increased RNase activity. Tobacco engineered to have an increased glutathione redox state exhibited substantially lower RNase activity during dark-induced senescence. These results suggest that RNase activity requires the presence of one or more disulfide bonds that are regulated by glutathione and demonstrate for the first time that RNase activity can be altered with an alteration in cellular redox state.

Influence of ozone on ribonuclease activity in wheat (Triticum aestivum) leaves

Ribonucleases (RNases) degrade RNA and exert a major influence on gene expression during development and in response to biotic and abiotic stresses. RNase activity typically increases in response to pathogen attack, wounding and phosphate (P(i)) deficiency. Activity also increases during senescence and other programmed cell death processes. The air pollutant ozone (O(3)) often induces injury and accelerated senescence in many plants, but the biochemical mechanisms involved in these responses remain unclear. The objective of this study was to determine whether RNase activity and isozyme expression was stimulated in wheat (Triticum aestivum L.) flag leaves following treatment with O(3). Plants were treated in open-top chambers with charcoal-filtered air (27 nmol O(3) mol(-1)) (control) or non-filtered air plus O(3) (90 nmol O(3) mol(-1)) (O(3)) from seedling to reproductive stage. After exposure for 56 days, RNase activity was 2.1 times higher in flag leaf tissues from an O(3)-sensitive cultivar in the O(3) treatment compared with the control, which generally coincided with foliar injury and lower soluble protein concentration, but not soluble leaf [P(i)]. Soluble [P(i)] in leaf tissue extracts from the O(3) and control treatments was not significantly different. RNase activity gels indicated the presence of three major RNases and two nucleases, and their expression was enhanced by the O(3) treatment. Isozymes stimulated in the O(3) treatment were also stimulated in naturally senescent flag leaf tissues from plants in the control. However, soluble [P(i)] in extracts from naturally senescent flag leaves was 50% lower than that found in green flag leaves in the control treatment. Thus, senescence-like pathological responses induced by O(3) were accompanied by increased RNase and nuclease activities that also were observed in naturally senescent leaves. However, [P(i)] in the leaf tissue samples suggested that O(3)-induced injury and accelerated senescence was atypical of normal senescence processes in that P(i) export was not observed in O(3)-treated plants.

Role of death in providing lifeline to plants

As the major transporters and distributors of water and minerals, xylem vessels and tracheids are the lifeline of plants. Interestingly, the building blocks of these water pipes are dead tracheary elements and vessel elements that have the process of cell death integrated into their differentiation programme. Using the Zinnia in vitro model system for xylogenesis, a key nuclease that is responsible for nuclear degradation during the terminal stages of tracheary element differentiation has been identified recently.

Endonuclease genes up-regulated in tissues undergoing programmed cell death are expressed during male gametogenesis in barley

In the process of programmed cell death (PCD), a key role has been attributed to endonucleases capable to cleave nuclear DNA at internucleosomal sites. In barley (Hordeum vulgare L.), two such nucleases (Bnuc1 and BEN1) were individually identified in unrelated tissues. In the present work, we demonstrate that their genes are also expressed in immature anthers at different stages of pollen development. Further experiments carried out on RNA extracted from immature barley anthers led to discover a novel endonuclease gene, namely Bnuc2 (AJ311603 in the EMBL/GenBank/DDBJ databases), eventually found up-regulated at the tetrad stage. The protein encoded was found to conserve large sequence portions of Bnuc1 and BEN1 endonucleases, including the domain regions involved in secretion and DNA/RNA binding. A survey conducted on barley EST libraries showed that Bnuc2 and BEN1 mRNAs are jointly present also in the transcriptome of 20 DAP spike and that other endonuclease ESTs are co-expressed with Bnuc1 or BEN1 in tissues where PCD has been recorded. Therefore, it can be concluded that during the PCD process, a set of S1-type endonucleases is synthesised regardless of the tissue considered.

Molecular cloning of two metallothionein-like protein genes with differential expression patterns from sweet potato (Ipomoea batatas) leaves

Metallothionein (MT) is a group of proteins with low molecular masses and high cysteine contents, and is classified into different types, which in general contains two domains (domain 1 and domain 2) with typical amino acid sequences (Rauser 1999). In this report two full-length cDNAs (Y459 and G14) encoding MT-like proteins were isolated from leaves of sweet potato (Ipomoea batatas). Their open reading frames contained 249 and 195 nucleotides (82 and 64 amino acids) for Y459 and G14, respectively, and exhibited a relatively low amino acid sequence similarity (ca. 25.8%). Gene structure studies showed that Y459 had the conserved domain 1 region of type 2 MT; however, the domain 2 region was not conserved and contained additional amino acids between the CxC and CxC spacing. G14 had conserved domains 1 and 2 of type 4 MT except that the last CxC of domain 2 was changed to RxC. Semi-quantitative RT-PCR showed that Y459 was expressed in significant quantity in roots and stems, but was much less in green leaves. During natural and induced (with dark and ethephon, an ethylene-releasing compound, treatments) leaf senescence, Y459 gene expression was significantly enhanced. In contrast, relatively constant gene expression levels were found for G14 in all tissues or treatments analyzed. In conclusion, the two MT-like protein genes of sweet potato display differential gene structures and gene expression patterns, which may be associated with the diverse roles and functions they play in plant physiology in order to cope with particular developmental and environmental cues.

Three-dimensional progression of programmed death in the rice coleoptile

Plant death during development is a highly orchestrated process at the cellular, tissue, organ, and whole-plant levels. The process toward death is endogenously programmed in plants. With our original approach called "three-dimensional analysis" using the rice coleoptile, we revealed detailed morphological alterations in the progression of senescence and programmed cell death involved in the air space (aerenchyma) formation at both tissue and cellular levels. Although these two types of cell death exhibited a distinct pattern of progression at the tissue level, the set of intracellular events was highly conserved. From those comprehensive investigations, we hypothesized that the identical program of death functions in each process of cell death, and that the initiation and progression of cell death is highly regulated by the environmental input.

The molecular analysis of leaf senescence--a genomics approach

Senescence in green plants is a complex and highly regulated process that occurs as part of plant development or can be prematurely induced by stress. In the last decade, the main focus of research has been on the identification of senescence mutants, as well as on genes that show enhanced expression during senescence. Analysis of these is beginning to expand our understanding of the processes by which senescence functions. Recent rapid advances in genomics resources, especially for the model plant species Arabidopsis, are providing scientists with a dazzling array of tools for the identification and functional analysis of the genes and pathways involved in senescence. In this review, we present the current understanding of the mechanisms by which plants control senescence and the processes that are involved.

ZEN1 is a key enzyme in the degradation of nuclear DNA during programmed cell death of tracheary elements

Tracheary elements (TEs) have a unique cell death program in which the rapid collapse of the vacuole triggers the beginning of nuclear degradation. Although various nucleases are known to function in nuclear DNA degradation in animal apoptosis, it is unclear what hydrolase is involved in nuclear degradation in plants. In this study, we demonstrated that an S1-type nuclease, Zinnia endonuclease 1 (ZEN1), functions directly in nuclear DNA degradation during programmed cell death (PCD) of TEs. In-gel DNase assay demonstrated the presence of a 24-kD Ca(2+)/Mg(2+)-dependent nuclease and a 40-kD Zn(2+)-dependent nuclease as well as ZEN1 in 60-h-cultured cells that included differentiating TEs. Such cell extracts possessed the ability to degrade the nuclear DNA isolated from Zinnia elegans cells in the presence of Zn(2+), and its activity was suppressed by an anti-ZEN1 antibody, indicating that ZEN1 is a central DNase responsible for nuclear DNA degradation. The introduction of the antisense ZEN1 gene into Zinnia cells cultured for 40 h specifically suppressed the degradation of nuclear DNA in TEs undergoing PCD but did not affect vacuole collapse. Based on these results, a common mechanism between animal and plant PCD is discussed.

Local and systemic wound-induction of RNase and nuclease activities in Arabidopsis: RNS1 as a marker for a JA-independent systemic signaling pathway

Induction of defense-related genes is one way in which plants respond to mechanical injury. We investigated whether RNases are involved in the wound response in Arabidopsis thaliana. As in other plant systems, several activities are induced with various timings in damaged leaves, stems and seedlings in Arabidopsis, including at least three bifunctional nucleases, capable of degrading both RNA and DNA, as well as RNS1, a member of the ubiquitous RNase T(2) family of RNases. The strong induction of RNS1 is particularly interesting because it occurs both locally and systemically following wounding. The systemic induction of this RNase indicates that members of this family may be involved in defense mechanisms in addition to their previously hypothesized functions in nutrient recycling and remobilization. Additionally, the systemic induction appears to be controlled independently of jasmonic acid, and the local induction of RNS1 and the nuclease activities are independent of both JA and oligosaccharide elicitors. Consequently, a novel systemic pathway, likely involving a third signal, appears to exist in Arabidopsis.

Identical promoter elements are involved in regulation of the OPR1 gene by senescence and jasmonic acid in Arabidopsis

Like other developmental processes, the terminal phase of leaf development, generally referred to as leaf senescence. regulates a subset of genes whose transcript abundances are increased during senescence. Jasmonic acid (JA), a plant growth regulator, also regulates the expression of subsets of genes in many aspects of plant growth and development, including leaf senescence. However, the underlying molecular mechanisms by which senescence and JA modulate gene expression are poorly understood. During an effort to isolate senescence-associated genes, we identified an Arabidopsis enhancer trap line in which the reporter gene GUS is up-regulated by both senescence and JA. The T-DNA tagged gene was subsequently cloned using thermal asymmetric interlaced PCR (TAIL-PCR). This gene encodes a 12-oxo-phytodienoic acid-10,11-reductase (OPR1). Consistent with the GUS expression data, RNA gel blot analysis showed that OPR1 was indeed up-regulated by both senescence and JA. Promoter deletion analysis and linker-scanning mutagenesis assays were employed to unveil the molecular bases of OPR1 regulation by senescence and JA. Two regulatory cis elements, namely JASE1 (5'-CGTCAATGAA-3') and JASE2 (5'-CATACGTCGTCAA-3'), in the promoter region of the gene, were identified. While JASE2 contains a mixed A/C box-like motif, JASE1 represents a new motif without any signature sequence so far reported. Both elements were required for the up-regulation of OPR1 by leaf senescence and JA. suggesting that leaf senescence and JA may share a common molecular mechanism for modulating OPR1.

The characterization of LeNUC1, a nuclease associated with leaf senescence of tomato

Induction of nuclease and RNase activities, together with decreases in nucleic acid content are considered to be characteristics of senescence in higher plants. However, little is known about the specific identities or functions of the enzymes involved or the mechanisms controlling their activation. Here we report the identification of a 41-kDa-tomato nuclease, LeNUC1, which is specifically induced during tomato leaf senescence but not in ripening fruits. LeNUC1 is a glycoprotein, which can degrade both RNA and DNA and has optimal activity at pH 7.5-8. EDTA inhibits the activity of LeNUC1, while the addition of Co2+ or Mn2+ can restore its activity in the presence of the chelating agent. Interestingly, the activity of LeNUC1 is also induced in young leaves upon treatment with ethylene, which is known to be a senescence-promoting hormone in tomato. Constitutive activity of a 39-kDa nuclease, LeNUC2, similar in its biochemical requirements to LeNUC1, was also detected. LeNUC2 is not induced by ethylene and does not seem to be glycosylated. Based on their characteristics, LeNUC1 and LeNUC2 can be classified as Nuclease I enzymes. LeNUC1 may be involved in nucleic acid metabolism during tomato leaf senescence.

Cloning and characterization of a receptor-like protein kinase gene associated with senescence

Senescence-associated genes are up-regulated during plant senescence and many have been implicated in encoding enzymes involved in the metabolism of senescing tissues. Using the differential display technique, we identified a SAG in bean (Phaseolus vulgaris) leaf that was exclusively expressed during senescence and was designated senescence-associated receptor-like kinase (SARK). The deduced SARK polypeptide consists of a signal peptide, a leucine-rich repeat in the extracellular region, a single membrane-spanning domain, and the characteristic serine/threonine protein kinase domain. The mRNA level for SARK increased prior to the loss of chlorophyll and the decrease of chlorophyll a/b-binding protein mRNA. Detached mature bean leaves, which senesce at an accelerated rate compared with leaves on intact plants, showed a similar temporal pattern of SARK message accumulation. Light and cytokinin, which delayed the initiation of leaf senescence, also delayed SARK gene expression; in contrast, darkness and ethylene, which accelerated senescence, advanced the initial appearance of the SARK transcript. SARK protein accumulation exhibited a temporal pattern similar to that of its mRNA. A possible role for SARK in the regulation of leaf senescence was considered.

Analysis of the G-overhang structures on plant telomeres: evidence for two distinct telomere architectures

Telomeres are highly conserved structures essential for maintaining the integrity of eukaryotic genomes. In yeast, ciliates and mammals, the G-rich strand of the telomere forms a 3' overhang on the chromosome terminus. Here we investigate the architecture of telomeres in the dicot plants Silene latifolia and Arabidopsis thaliana using the PENT (primer extension/nick translation) assay. We show that both Arabidopsis and Silene telomeres carry G-overhangs longer than 20-30 nucleotides. However, in contrast to yeast and ciliate telomeres, only half of the telomeres in Silene seedlings possess detectable G-overhangs. PENT reactions using a variety of primers and reaction conditions revealed that the remaining fraction of Silene telomeres carries either no overhangs or overhangs less than 12 nucleotides in length. G-overhangs were observed in Silene seeds and leaves, tissues that lack telomerase activity. These findings suggest that incomplete DNA replication of the lagging strand, rather than synthesis by telomerase, is the primary mechanism for G-overhang synthesis in plants. Unexpectedly, we found that the fraction of telomeres with detectable G-overhangs decreased from 50% in seedlings to 35% in leaves. The difference may reflect increased susceptibility of the G-overhangs to nuclease attack in adult leaves, an event that could act as a precursor for the catabolic processes accompanying leaf senescence