Telomere dynamics and oxidative stress in Arabidopsis grown in lunar regolith simulant

NASA envisions a future where humans establish a thriving colony on the Moon by 2050. Plants will be essential for this endeavor, but little is known about their adaptation to extraterrestrial bodies. The capacity to grow plants in lunar regolith would represent a major step towards this goal by minimizing the reliance on resources transported from Earth. Recent studies reveal that Arabidopsis thaliana can germinate and grow on genuine lunar regolith as well as on lunar regolith simulant. However, plants arrest in vegetative development and activate a variety of stress response pathways, most notably the oxidative stress response. Telomeres are hotspots for oxidative damage in the genome and a marker of fitness in many organisms. Here we examine A. thaliana growth on a lunar regolith simulant and the impact of this resource on plant physiology and on telomere dynamics, telomerase enzyme activity and genome oxidation. We report that plants successfully set seed and generate a viable second plant generation if the lunar regolith simulant is pre-washed with an antioxidant cocktail. However, plants sustain a higher degree of genome oxidation and decreased biomass relative to conventional Earth soil cultivation. Moreover, telomerase activity substantially declines and telomeres shorten in plants grown in lunar regolith simulant, implying that genome integrity may not be sustainable over the long-term. Overcoming these challenges will be an important goal in ensuring success on the lunar frontier.

Arabidopsis telomerase takes off by uncoupling enzyme activity from telomere length maintenance in space

Spaceflight-induced changes in astronaut telomeres have garnered significant attention in recent years. While plants represent an essential component of future long-duration space travel, the impacts of spaceflight on plant telomeres and telomerase have not been examined. Here we report on the telomere dynamics of Arabidopsis thaliana grown aboard the International Space Station. We observe no changes in telomere length in space-flown Arabidopsis seedlings, despite a dramatic increase in telomerase activity (up to 150-fold in roots), as well as elevated genome oxidation. Ground-based follow up studies provide further evidence that telomerase is induced by different environmental stressors, but its activity is uncoupled from telomere length. Supporting this conclusion, genetically engineered super-telomerase lines with enhanced telomerase activity maintain wildtype telomere length. Finally, genome oxidation is inversely correlated with telomerase activity levels. We propose a redox protective capacity for Arabidopsis telomerase that may promote survivability in harsh environments.

Quantification of 8-oxoG in Plant Telomeres

Chemical modifications in DNA impact gene regulation and chromatin structure. DNA oxidation, for example, alters gene expression, DNA synthesis and cell cycle progression. Modification of telomeric DNA by oxidation is emerging as a marker of genotoxic damage and is associated with reduced genome integrity and changes in telomere length and telomerase activity. 8-oxoguanine (8-oxoG) is the most studied and common outcome of oxidative damage in DNA. The G-rich nature of telomeric DNA is proposed to make it a hotspot for oxidation, but because telomeres make up only a tiny fraction of the genome, it has been difficult to directly test this hypothesis by studying dynamic DNA modifications specific to this region in vivo. Here, we present a new, robust method to differentially enrich telomeric DNA in solution, coupled with downstream methods for determination of chemical modification. Specifically, we measure 8-oxoG in Arabidopsis thaliana telomeres under normal and oxidative stress conditions. We show that telomere length is unchanged in response to oxidative stress in three different wild-type accessions. Furthermore, we report that while telomeric DNA comprises only 0.02–0.07% of the total genome, telomeres contribute between 0.2 and 15% of the total 8-oxoG. That is, plant telomeres accumulate 8-oxoG at levels approximately 100-fold higher than the rest of the genome under standard growth conditions. Moreover, they are the primary targets of further damage upon oxidative stress. Interestingly, the accumulation of 8-oxoG in the chromosome body seems to be inversely proportional to telomere length. These findings support the hypothesis that telomeres are hotspots of 8-oxoG and may function as sentinels of oxidative stress in plants.

Arabidopsis retains vertebrate-type telomerase accessory proteins via a plant-specific assembly

The recent discovery of the bona-fide telomerase RNA (TR) from plants reveals conserved and unique secondary structure elements and the opportunity for new insight into the telomerase RNP. Here we examine how two highly conserved proteins previously implicated in Arabidopsis telomere maintenance, AtPOT1a and AtNAP57 (dyskerin), engage plant telomerase. We report that AtPOT1a associates with Arabidopsis telomerase via interaction with TERT. While loss of AtPOT1a does not impact AtTR stability, the templating domain is more accessible in pot1a mutants, supporting the conclusion that AtPOT1a stimulates telomerase activity but does not facilitate telomerase RNP assembly. We also show, that despite the absence of a canonical H/ACA binding motif within AtTR, dyskerin binds AtTR with high affinity and specificity in vitro via a plant specific three-way junction (TWJ). A core element of the TWJ is the P1a stem, which unites the 5′ and 3′ ends of AtTR. P1a is required for dyskerin-mediated stimulation of telomerase repeat addition processivity in vitro, and for AtTR accumulation and telomerase activity in vivo. The deployment of vertebrate-like accessory proteins and unique RNA structural elements by Arabidopsis telomerase provides a new platform for exploring telomerase biogenesis and evolution.

Change and HOAP for the best

HOAP is a telomere-binding protein that has a conserved role in Drosophila, but it also needs to evolve quickly to restrict telomeric retrotransposons.

tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana

KEY MESSAGE: tRNA Adenosine Deaminase 3 helps to sustain telomere tracts in a telomerase-independent fashion, likely through regulating cellular metabolism. Telomere length maintenance is influenced by a complex web of chromatin and metabolism-related factors. We previously reported that a lncRNA termed AtTER2 regulates telomerase activity in Arabidopsis thaliana in response to DNA damage. AtTER2 was initially shown to partially overlap with the 5' UTR of the tRNA ADENOSINE DEAMINASE 3 (TAD3) gene. However, updated genome annotation showed that AtTER2 was completely embedded in TAD3, raising the possibility that phenotypes ascribed to AtTER2 could be derived from TAD3. Here we show through strand-specific RNA-Seq, strand-specific qRT-PCR and bioinformatic analyses that AtTER2 does not encode a stable lncRNA. Further examination of the original tad3 (ter2-1/tad3-1) mutant revealed expression of an antisense transcript driven by a cryptic promoter in the T-DNA. Hence, a new hypomorphic allele of TAD3 (tad3-2) was examined. tad3-2 mutants showed hypersensitivity to DNA damage, but no deregulation of telomerase, suggesting that the telomerase phenotype of tad3-1 mutants reflects an off-target effect. Unexpectedly, however, tad3-2 plants displayed progressive loss of telomeric DNA over successive generations that was not accompanied by alteration of terminal architecture or end protection. The phenotype was exacerbated in plants lacking the telomerase processivity factor POT1a, indicating that TAD3 promotes telomere maintenance through a non-canonical, telomerase-independent pathway. The transcriptome of tad3-2 mutants revealed significant dysregulation of genes involved in auxin signaling and glucosinolate biosynthesis, pathways that intersect the stress response, cell cycle regulation and DNA metabolism. These findings indicate that the TAD3 locus indirectly contributes to telomere length homeostasis by altering the metabolic profile in Arabidopsis.

The conserved structure of plant telomerase RNA provides the missing link for an evolutionary pathway from ciliates to humans

Telomerase is essential for maintaining telomere integrity. Although telomerase function is widely conserved, the integral telomerase RNA (TR) that provides a template for telomeric DNA synthesis has diverged dramatically. Nevertheless, TR molecules retain 2 highly conserved structural domains critical for catalysis: a template-proximal pseudoknot (PK) structure and a downstream stem-loop structure. Here we introduce the authentic TR from the plant Arabidopsis thaliana, called AtTR, identified through next-generation sequencing of RNAs copurifying with Arabidopsis TERT. This RNA is distinct from the RNA previously described as the templating telomerase RNA, AtTER1. AtTR is a 268-nt Pol III transcript necessary for telomere maintenance in vivo and sufficient with TERT to reconstitute telomerase activity in vitro. Bioinformatics analysis identified 85 AtTR orthologs from 3 major clades of plants: angiosperms, gymnosperms, and lycophytes. Through phylogenetic comparisons, a secondary structure model conserved among plant TRs was inferred and verified using in vitro and in vivo chemical probing. The conserved plant TR structure contains a template-PK core domain enclosed by a P1 stem and a 3' long-stem P4/5/6, both of which resemble a corresponding structural element in ciliate and vertebrate TRs. However, the plant TR contains additional stems and linkers within the template-PK core, allowing for expansion of PK structure from the simple PK in the smaller ciliate TR during evolution. Thus, the plant TR provides an evolutionary bridge that unites the disparate structures of previously characterized TRs from ciliates and vertebrates.

Recent emergence and extinction of the protection of telomeres 1c gene in Arabidopsis thaliana

Duplicate POT1 genes must rapidly diverge or be inactivated. Protection of telomeres 1 (POT1) encodes a conserved telomere binding protein implicated in both chromosome end protection and telomere length maintenance. Most organisms harbor a single POT1 gene, but in the few lineages where the POT1 family has expanded, the duplicate genes have diversified. Arabidopsis thaliana bears three POT1-like loci, POT1a, POT1b and POT1c. POT1a retains the ancestral function of telomerase regulation, while POT1b is implicated in chromosome end protection. Here we examine the function and evolution of the third POT1 paralog, POT1c. POT1c is a new gene, unique to A. thaliana, and was derived from a duplication event involving the POT1a locus and a neighboring gene encoding ribosomal protein S17. The duplicate S17 locus (dS17) is highly conserved across A. thaliana accessions, while POT1c is highly divergent, harboring multiple deletions within the gene body and two transposable elements within the promoter. The POT1c locus is transcribed at very low to non-detectable levels under standard growth conditions. In addition, no discernable molecular or developmental defects are associated with plants bearing a CRISPR mutation in the POT1c locus. However, forced expression of POT1c leads to decreased telomerase enzyme activity and shortened telomeres. Evolutionary reconstruction indicates that transposons invaded the POT1c promoter soon after the locus was formed, permanently silencing the gene. Altogether, these findings argue that POT1 dosage is critically important for viability and duplicate gene copies are retained only upon functional divergence.

The Trojan Horse of the Plant Kingdom

The advent of host-induced gene silencing (HIGS) technology for the development of pathogen-resistant cultivars led to the discovery of cross-kingdom RNA interference. In a recent Science paper, Cai et al. (2018) discovered that plant extracellular vesicles act as Trojan horses to deliver small RNAs into fungi to fight infection.

βC1 protein encoded in geminivirus satellite concertedly targets MKK2 and MPK4 to counter host defense

Plant viruses have evolved multiple strategies to overcome host defense to establish an infection. Here, we identified two components of a host mitogen-activated protein kinase (MAPK) cascade, MKK2 and MPK4, as bona fide targets of the βC1 protein encoded by the betasatellite of tomato yellow leaf curl China virus (TYLCCNV). βC1 interacts with the kinase domain of MKK2 and inhibits its activity. In vivo, βC1 suppresses flagellin-induced MAPK activation and downstream responses by targeting MKK2. Furthermore, βC1 also interacts with MPK4 and inhibits its kinase activity. TYLCCNV infection induces the activation of the MAPK cascade, mutation in MKK2 or MPK4 renders the plant more susceptible to TYLCCNV, and can complement the lack of βC1. This work shows for the first time that a plant virus both activates and suppresses a MAPK cascade, and the discovery of the ability of βC1 to selectively interfere with the host MAPK activation illustrates a novel virulence function and counter-host defense mechanism of geminiviruses.

Genome-Wide Investigation of the Role of MicroRNAs in Desiccation Tolerance in the Resurrection Grass Tripogon loliiformis

Drought causes approximately two-thirds of crop and yield loss worldwide. To sustain future generations, there is a need to develop robust crops with enhanced water use efficiency. Resurrection plants are naturally resilient and tolerate up to 95% water loss with the ability to revive upon watering. Stress is genetically encoded and resilient species may garner tolerance by tightly regulating the expression of stress-related genes. MicroRNAs (miRNAs) post-transcriptionally regulate development and other stress response processes in eukaryotes. However, their role in resurrection plant desiccation tolerance is poorly understood. In this study, small RNA sequencing and miRNA expression profiling was conducted using Tripogon loliiformis plants subjected to extreme water deficit conditions. Differentially expressed miRNA profiles, target mRNAs, and their regulatory processes were elucidated. Gene ontology enrichment analysis revealed that development, stress response, and regulation of programmed cell death biological processes; Oxidoreductase and hydrolyase molecular activities; and SPL, MYB, and WRKY transcription factors were targeted by miRNAs during dehydration stress, indicating the indispensable regulatory role of miRNAs in desiccation tolerance. This study provides insights into the molecular mechanisms of desiccation tolerance in the resurrection plant T. loliiformis. This information will be useful in devising strategies for crop improvement on enhanced drought tolerance and water use efficiency.

Arabidopsis Serrate Coordinates Histone Methyltransferases ATXR5/6 and RNA Processing Factor RDR6 to Regulate Transposon Expression

Serrate (SE) is a key component in RNA metabolism. Little is known about whether and how it can regulate epigenetic silencing. Here, we report histone methyltransferases ATXR5 and ATXR6 (ATXR5/6) as novel partners of SE. ATXR5/6 deposit histone 3 lysine 27 monomethylation (H3K27me1) to promote heterochromatin formation, repress transposable elements (TEs), and control genome stability in Arabidopsis. SE binds to ATXR5/6-regulated TE loci and promotes H3K27me1 accumulation in these regions. Furthermore, SE directly enhances ATXR5 enzymatic activity in vitro. Unexpectedly, se mutation suppresses the TE reactivation and DNA re-replication phenotypes in the atxr5 atxr6 mutant. The suppression of TE expression results from triggering RNA-dependent RNA polymerase 6 (RDR6)-dependent RNA silencing in the se atxr5 atxr6 mutant. We propose that SE facilitates ATXR5/6-mediated deposition of the H3K27me1 mark while inhibiting RDR6-mediated RNA silencing to protect TE transcripts. Hence, SE coordinates epigenetic silencing and RNA processing machineries to fine-tune the TE expression.

RISC-interacting clearing 3'- 5' exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis thaliana

RNA-induced silencing complex (RISC) is composed of miRNAs and AGO proteins. AGOs use miRNAs as guides to slice target mRNAs to produce truncated 5' and 3' RNA fragments. The 5' cleaved RNA fragments are marked with uridylation for degradation. Here, we identified novel cofactors of Arabidopsis AGOs, named RICE1 and RICE2. RICE proteins specifically degraded single-strand (ss) RNAs in vitro; but neither miRNAs nor miRNA*s in vivo. RICE1 exhibited a DnaQ-like exonuclease fold and formed a homohexamer with the active sites located at the interfaces between RICE1 subunits. Notably, ectopic expression of catalytically-inactive RICE1 not only significantly reduced miRNA levels; but also increased 5' cleavage RISC fragments with extended uridine tails. We conclude that RICEs act to degrade uridylated 5’ products of AGO cleavage to maintain functional RISC. Our study also suggests a possible link between decay of cleaved target mRNAs and miRNA stability in RISC.

DOI:http://dx.doi.org/10.7554/eLife.24466.001

DNA contains all the information needed to build a body, yet molecules of RNA carry these instructions to the sites in the cell where they can be used. Cells must control how much RNA they produce in order to ensure that they develop properly and can respond well to their environment. RNA silencing refers to a collection of mechanisms that use smaller RNA molecules called microRNAs to incapacitate certain RNA molecules and selectively switch off the genes that encode them to stop more from being made.

One key player in RNA silencing is the multi-protein complex called RISC, which contains microRNA and a group of proteins called AGOs. Once the microRNA has identified its RNA target, the AGOs cut the RNA into two pieces, known as the 5’ cleavage fragment and 3’ cleavage fragment. The two resulting fragments need to be cleared away swiftly, so that the RISC can move on to the next target. While it was known how the 3’ cleavage fragment was removed, it was less clear how the 5’ cleavage fragment was dealt with.

Previous studies had shown that the 5’ cleavage fragment was marked with a chemical called uridine, which somehow signals to the RISC that this fragment needs to be destroyed. Now, using biochemical techniques, Zhang et al. have identified two new proteins in the model plant Arabidopsis that attach to the AGO proteins and degrade the 5’ cleavage fragments that are marked with uridine. The two proteins are named RICE1 and RICE2.

Zhang et al. then analyzed the three-dimensional shape of RICE1 and identified the ‘active’ region that is responsible for degrading the RNA fragments. When these active regions were blocked, the microRNA levels were low, but the uridine-marked 5’ cleavage fragments were high. Also, the RISC complex could not work properly, which lead to problems during the development of the plant. These results suggest that RICE proteins degrade 5’ cleavage fragments modified with uridine to activate RISC.

RICE proteins are conserved between plants and animals, and it is likely that their counterparts in humans will have a similar role to the plant proteins. The next challenge will be to explore how RICE proteins work in more details, which may lead to new ways to manipulate the levels of microRNAs to change the architecture of the plant and to improve their tolerance to various stress conditions.

DOI:http://dx.doi.org/10.7554/eLife.24466.002

The functions of plant small RNAs in development and in stress responses

Like metazoans, plants use small regulatory RNAs (sRNAs) to direct gene expression. Several classes of sRNAs, which are distinguished by their origin and biogenesis, exist in plants. Among them, microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs) mainly inhibit gene expression at post-transcriptional levels. In the past decades, plant miRNAs and ta-siRNAs have been shown to be essential for numerous developmental processes, including growth and development of shoots, leaves, flowers, roots and seeds, among others. In addition, miRNAs and ta-siRNAs are also involved in the plant responses to abiotic and biotic stresses, such as drought, temperature, salinity, nutrient deprivation, bacteria, virus and others. This review summarizes the roles of miRNAs and ta-siRNAs in plant physiology and development.

Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense

Transcriptional gene silencing (TGS) can serve as an innate immunity against invading DNA viruses throughout Eukaryotes. Geminivirus code for TrAP protein to suppress the TGS pathway. Here, we identified an Arabidopsis H3K9me2 histone methyltransferase, Su(var)3-9 homolog 4/Kryptonite (SUVH4/KYP), as a bona fide cellular target of TrAP. TrAP interacts with the catalytic domain of KYP and inhibits its activity in vitro. TrAP elicits developmental anomalies phenocopying several TGS mutants, reduces the repressive H3K9me2 mark and CHH DNA methylation, and reactivates numerous endogenous KYP-repressed loci in vivo. Moreover, KYP binds to the viral chromatin and controls its methylation to combat virus infection. Notably, kyp mutants support systemic infection of TrAP-deficient Geminivirus. We conclude that TrAP attenuates the TGS of the viral chromatin by inhibiting KYP activity to evade host surveillance. These findings provide new insight on the molecular arms race between host antiviral defense and virus counter defense at an epigenetic level.

DOI:http://dx.doi.org/10.7554/eLife.06671.001

Many viruses can infect plants and cause diseases that can reduce crop yields. The Geminiviruses are a family of plant viruses that are transmitted by insects and infect tomato, cabbage, and many other crop plants. These viruses hijack the plant cells that they infect and force the plant cells to make viral proteins using instructions provided by the genes in the virus' own DNA. To make proteins, DNA is first copied into molecules of messenger ribonucleic acid (or mRNA) in a process called transcription. However, plants can defend themselves by blocking the transcription of viral DNA through ‘transcriptional gene silencing’.

In plant cells, DNA is packaged around proteins called histones to form a structure called chromatin. Small chemical tags attached to the histones can alter the structure of chromatin to regulate the activity of the genes encoded within it. For example, ‘methyl’ tags added to certain histones can block transcription and lower the activity of a gene. DNA from viruses can also associate with histones inside plant cells meaning that transcriptional gene silencing can take place by the addition of these methyl tags. Many Geminiviruses produce a protein called TrAP, which can activate transcription, but it is not clear how this works.

Castillo-González et al. studied the TrAP proteins from two different Geminiviruses that can infect crop plants. The commonly used model plant, Arabidopsis thaliana, was genetically engineered to produce high levels of these TrAP proteins. These ‘transgenic’ plants did not develop properly: they grew more slowly, had abnormal leaves, and flowered earlier. Furthermore, hundreds of plant genes were more active than usual in the transgenic plants, which suggests that TrAP inhibits transcriptional gene silencing. Further experiments showed that TrAP directly binds to a plant enzyme called KYP—which normally deposits methyl groups on chromatin and prevents it from working. This reduces the number of methyl groups that are attached to histones associated with both viral and plant chromatin, which results in the activation of genes that would normally be switched off.

Castillo-González et al.'s findings show how Geminiviruses can stop transcriptional gene silencing of chromatin that contains virus DNA to evade the host plant's defenses. The next challenge is to understand how TrAP inhibits KYP, which may present new ways to genetically engineer plants to become resistant to infection by viruses.

DOI:http://dx.doi.org/10.7554/eLife.06671.002

Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1

miRNAs originate from primary transcripts (pri-miRNAs) with characteristic stem-loop structures. Accurate processing of pri-miRNAs is required for functional miRNAs. Here, using pri-miR166 family as a paradigm, we report the decisive role of pri-miRNA terminal loops in miRNA biogenesis. We found that multi-branched terminal loops in pri-miR166s substantially suppressed miR166 expression in vivo. Unlike canonical processing of pri-miRNAs, terminal-loop-branched (TLBed) pri-miRNAs can be processed by Dicer-like1 (DCL1) complexes bi-directionally: from base to loop and from loop to base, resulting in productive and abortive processing of miRNAs, respectively. In either case, DCL1 complexes canonically cut pri-miRNAs at a distance of 16-17 base pairs (bp) from a reference single-stranded loop region. DCL1 also adjusts processing sites toward an internal loop through its helicase domain. Thus, these results provide new insight into the poorly understood processing mechanism of pri-miRNAs with complicated secondary structures.