RPW8/HR repeats control NLR activation in Arabidopsis thaliana.

In many plant species, conflicts between divergent elements of the immune system, especially nucleotide-binding oligomerization domain-like receptors (NLR), can lead to hybrid necrosis. Here, we report deleterious allele-specific interactions between an NLR and a non-NLR gene cluster, resulting in not one, but multiple hybrid necrosis cases in Arabidopsis thaliana. The NLR cluster is RESISTANCE TO PERONOSPORA PARASITICA 7 (RPP7), which can confer strain-specific resistance to oomycetes. The non-NLR cluster is RESISTANCE TO POWDERY MILDEW 8 (RPW8) / HOMOLOG OF RPW8 (HR), which can confer broad-spectrum resistance to both fungi and oomycetes. RPW8/HR proteins contain at the N-terminus a potential transmembrane domain, followed by a specific coiled-coil (CC) domain that is similar to a domain found in pore-forming toxins MLKL and HET-S from mammals and fungi. C-terminal to the CC domain is a variable number of 21- or 14-amino acid repeats, reminiscent of regulatory 21-amino acid repeats in fungal HET-S. The number of repeats in different RPW8/HR proteins along with the sequence of a short C-terminal tail predicts their ability to activate immunity in combination with specific RPP7 partners. Whether a larger or smaller number of repeats is more dangerous depends on the specific RPW8/HR autoimmune risk variant.

FTIP1 is an essential regulator required for florigen transport.

The capacity to respond to day length, photoperiodism, is crucial for flowering plants to adapt to seasonal change. The photoperiodic control of flowering in plants is mediated by a long-distance mobile floral stimulus called florigen that moves from leaves to the shoot apex. Although the proteins encoded by FLOWERING LOCUS T (FT) in Arabidopsis and its orthologs in other plants are identified as the long-sought florigen, whether their transport is a simple diffusion process or under regulation remains elusive. Here we show that an endoplasmic reticulum (ER) membrane protein, FT-INTERACTING PROTEIN 1 (FTIP1), is an essential regulator required for FT protein transport in Arabidopsis. Loss of function of FTIP1 exhibits late flowering under long days, which is partly due to the compromised FT movement to the shoot apex. FTIP1 and FT share similar mRNA expression patterns and subcellular localization, and they interact specifically in phloem companion cells. FTIP1 is required for FT export from companion cells to sieve elements, thus affecting FT transport through the phloem to the SAM. Our results provide a mechanistic understanding of florigen transport, demonstrating that FT moves in a regulated manner and that FTIP1 mediates FT transport to induce flowering.

A zinc finger protein gene ZFP5 integrates phytohormone signaling to control root hair development in Arabidopsis.

Although root hair development in Arabidopsis thaliana has been extensively studied, it remains unknown whether the zinc finger proteins, the largest family of transcription factors in plants, are involved in this process. Here we report that the C2H2 zinc finger protein ZINC FINGER PROTEIN 5 (ZFP5) is a key regulator of root hair initiation and morphogenesis in Arabidopsis. ZFP5 is mainly expressed in root and preferentially in root hair cells. Using both zfp5 mutants and ZFP5 RNAi lines, we show that reduction in ZFP5 function leads to fewer and much shorter root hairs compared to wild-type. Genetic and molecular experiments demonstrate that ZFP5 exerts its effect on root hair development by directly promoting expression of the CAPRICE (CPC) gene. Furthermore, we show that ZFP5 expression is induced by cytokinin, and that ZFP5 mediates cytokinin and ethylene effects on the formation and growth of root hairs. These results suggest that ZFP5 integrates various plant hormone cues to control root epidermal cell development in Arabidopsis.

MOTHER OF FT AND TFL1 regulates seed germination through a negative feedback loop modulating ABA signaling in Arabidopsis.

Abscisic acid (ABA) and gibberellin (GA) are two antagonistic phytohormones that regulate seed germination in response to biotic and abiotic environmental stresses. We demonstrate here that MOTHER OF FT AND TFL1 (MFT), which encodes a phosphatidylethanolamine-binding protein, regulates seed germination via the ABA and GA signaling pathways in Arabidopsis thaliana. MFT is specifically induced in the radical-hypocotyl transition zone of the embryo in response to ABA, and mft loss-of-function mutants show hypersensitivity to ABA in seed germination. In germinating seeds, MFT expression is directly regulated by ABA-INSENSITIVE3 (ABI3) and ABI5, two key transcription factors in ABA signaling pathway. MFT is also upregulated by DELLA proteins in the GA signaling pathway. MFT in turn provides negative feedback regulation of ABA signaling by directly repressing ABI5. We conclude that during seed germination, MFT promotes embryo growth by constituting a negative feedback loop in the ABA signaling pathway.

Zinc finger protein5 is required for the control of trichome initiation by acting upstream of zinc finger protein8 in Arabidopsis.

Arabidopsis (Arabidopsis thaliana) trichome development is a model system for studying cell development, cell differentiation, and the cell cycle. Our previous studies have shown that the GLABROUS INFLORESCENCE STEMS (GIS) family genes, GIS, GIS2, and ZINC FINGER PROTEIN8 (ZFP8), control shoot maturation and epidermal cell fate by integrating gibberellins (GAs) and cytokinin signaling in Arabidopsis. Here, we show that a new C2H2 zinc finger protein, ZFP5, plays an important role in controlling trichome cell development through GA signaling. Overexpression of ZFP5 results in the formation of ectopic trichomes on carpels and other inflorescence organs. zfp5 loss-of-function mutants exhibit a reduced number of trichomes on sepals, cauline leaves, paraclades, and main inflorescence stems in comparison with wild-type plants. More importantly, it is found that ZFP5 mediates the regulation of trichome initiation by GAs. These results are consistent with ZFP5 expression patterns and the regional influence of GA on trichome initiation. The molecular analyses suggest that ZFP5 functions upstream of GIS, GIS2, ZFP8, and the key trichome initiation regulators GLABROUS1 (GL1) and GL3. Using a steroid-inducible activation of ZFP5 and chromatin immunoprecipitation experiments, we further demonstrate that ZFP8 is the direct target of ZFP5 in controlling epidermal cell differentiation.

An efficient CRISPR vector toolbox for engineering large deletions in Arabidopsis thaliana.

BACKGROUND: Our knowledge of natural genetic variation is increasing at an extremely rapid pace, affording an opportunity to come to a much richer understanding of how effects of specific genes are dependent on the genetic background. To achieve a systematic understanding of such GxG interactions, it is desirable to develop genome editing tools that can be rapidly deployed across many different genetic varieties. RESULTS: We present an efficient CRISPR/Cas9 toolbox of super module (SM) vectors. These vectors are based on a previously described fluorescence protein marker expressed in seeds allowing identification of transgene-free mutants. We have used this vector series to delete genomic regions ranging from 1.7 to 13 kb in different natural accessions of the wild plant Arabidopsis thaliana. Based on results from 53 pairs of sgRNAs targeting individual nucleotide binding site leucine-rich repeat (NLR) genes, we provide a comprehensive overview of obtaining heritable deletions. CONCLUSIONS: The SM series of CRISPR/Cas9 vectors enables the rapid generation of transgene-free, genome edited plants for a diversity of functional studies.

Bacterial community composition of a shallow hypertrophic freshwater lake in China, revealed by 16S rRNA gene sequences.

The phylogenetic composition of a bacterial community from a hypertrophic freshwater lake in China was investigated by sequencing cloned 16S rRNA genes. Three hundred and thirty-six bacterial clones from four clone libraries in different months (March, May, July and September in 2004) were classified into 142 operational taxonomic units, most of which were affiliated with bacterial divisions commonly found in freshwater ecosystem, e.g. Alpha-, Beta-, Gamma- and Deltaproteobacteria, Bacteriodetes and Actinobacteria. The results showed that the composition of bacterial community in the July library was the most diverse one. Actinobacteria was the most significant lineage in Lake Taihu, with dominant numbers of operational taxonomic units in the May, July and September libraries. Phylogenetic analysis suggested that 53 sequences were grouped into six novel clusters which may represent specific populations indigenous to the environment. Coverage analyses indicated that the clone libraries could provide a fine inventory of bacterial diversity in the lake.

Pin1At regulates PIN1 polar localization and root gravitropism.

Root gravitropism allows plants to establish root systems and its regulation depends on polar auxin transport mediated by PIN-FORMED (PIN) auxin transporters. PINOID (PID) and PROTEIN PHOSPHATASE 2A (PP2A) act antagonistically on reversible phosphorylation of PINs. This regulates polar PIN distribution and auxin transport. Here we show that a peptidyl-prolyl cis/trans isomerase Pin1At regulates root gravitropism. Downregulation of Pin1At suppresses root agravitropic phenotypes of pp2aa and 35S:PID, while overexpression of Pin1At affects root gravitropic responses and enhances the pp2aa agravitropic phenotype. Pin1At also affects auxin transport and polar localization of PIN1 in stele cells, which is mediated by PID and PP2A. Furthermore, Pin1At catalyses the conformational change of the phosphorylated Ser/Thr-Pro motifs of PIN1. Thus, Pin1At mediates the conformational dynamics of PIN1 and affects PID- and PP2A-mediated regulation of PIN1 polar localization, which correlates with the regulation of root gravitropism.

A conserved genetic pathway determines inflorescence architecture in Arabidopsis and rice.

The spatiotemporal architecture of inflorescences that bear flowers determines plant reproductive success by affecting fruit set and plant interaction with pollinators. The inflorescence architecture that displays great diversity across flowering plants depends on developmental decisions at inflorescence meristems. Here we report a key conserved genetic pathway determining inflorescence architecture in Arabidopsis thaliana and Oryza sativa (rice). In Arabidopsis, four MADS-box genes, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1, SHORT VEGETATIVE PHASE, AGAMOUS-LIKE 24, and SEPALLATA 4 act redundantly and directly to suppress TERMINAL FLOWER1 (TFL1) in emerging floral meristems. This is indispensable for the well-known function of APETALA1 in specifying floral meristems and is coupled with a conformational change in chromosome looping at the TFL1 locus. Similarly, we demonstrate that the orthologs of these MADS-box genes in rice determine panicle branching by regulating TFL1-like genes. Our findings reveal a conserved regulatory pathway that determines inflorescence architecture in flowering plants.

MOTHER OF FT AND TFL1 regulates seed germination and fertility relevant to the brassinosteroid signaling pathway.

Brassinosteroids (BRs) are a family of plant steroid hormones that play diverse roles in many aspects of plant growth and development. For example, BRs promote seed germination by counteracting the inhibitory effect of ABA and regulate plant reproductive development, thus affecting seed yield. We have recently reported that MOTHER OF FT AND TFL1 (MFT) regulates seed germination through a negative feedback loop modulating ABA signaling in Arabidopsis. Here, we show that MFT function is also relevant to the BR signaling pathway. In mft loss-of-function mutants, the application of BR could not fully antagonize the inhibitory effect of exogenous ABA on seed germination, suggesting that BR promotes seed germination against ABA partly through MFT. In addition, mft enhances the low-fertility phenotype of det2 in which BR biosynthesis is blocked. This phenotype, together with the observation that MFT is expressed in gametophytes and developing seeds, suggests that MFT and BR play redundant roles in regulating fertility. Therefore, these results suggest that MFT affects seed germination and fertility relevant to the BR signaling pathway.

An expanding list: another flowering time gene, FLOWERING LOCUS T, regulates flower development.

The beauty of flowers requires proper floral patterning, during which the temporal and spatial expression of floral homeotic genes are regulated to specify floral organs in floral meristems. Regulation of floral patterning early occurs in emerging floral primordia, which is prior to the emergence of floral organs and mediated by an ever-expanding list of regulators. We have recently reported the regulation of floral patterning by a new genetic pathway governed by three flowering time genes, SHORT VEGETATIVE PHASE (SVP), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and AGAMOUS-LIKE 24 (AGL24). Here we show that another key flowering time gene, FLOWERING LOCUS T (FT), is also involved in regulating floral patterning. Our results suggest that flowering time genes are important regulators in the whole process of flower ontogeny from initial specification of incipient floral primordia to flower differentiation.

Regulation of floral patterning by flowering time genes.

Floral patterning in Arabidopsis requires activation of floral homeotic genes by the floral meristem identity gene, LEAFY (LFY). Here we show that precise activation of expression of class B and C homeotic genes in floral meristems is regulated by three flowering time genes, SHORT VEGETATIVE PHASE (SVP), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), and AGAMOUS-LIKE 24 (AGL24), through direct control of a LFY coregulator, SEPALLATA3 (SEP3). Orchestrated repression of SEP3 by SVP, AGL24, and SOC1 is mediated by recruiting two interacting chromatin regulators, TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1 and SAP18, a member of SIN3 histone deacetylase complex. Our finding of coordinated regulation of SEP3 by flowering time genes reveals a hitherto unknown genetic pathway that prevents premature differentiation of floral meristems and determines the appropriate timing of floral organ patterning.