AtHB40 modulates primary root length and gravitropism involving CYCLINB and auxin transporters.

Gravitropism is a finely regulated tropistic response based on the plant perception of directional cues. Such perception allows them to direct shoot growth upwards, above ground, and root growth downwards, into the soil, anchoring the plant to acquire water and nutrients. Gravity sensing occurs in specialized cells and depends on auxin distribution, regulated by influx/efflux carriers. Here we report that AtHB40, encoding a transcription factor of the homeodomain-leucine zipper I family, was expressed in the columella and the root tip. Athb40 mutants exhibited longer primary roots. Enhanced primary root elongation was in agreement with a higher number of cells in the transition zone and the induction of CYCLINB transcript levels. Moreover, athb40 mutants and AtHB40 overexpressors displayed enhanced and delayed gravitropistic responses, respectively. These phenotypes were associated with altered auxin distribution and deregulated expression of the auxin transporters LAX2, LAX3, and PIN2. Accordingly, lax2 and lax3 mutants also showed an altered gravitropistic response, and LAX3 was identified as a direct target of AtHB40. Furthermore, AtHB40 is induced by AtHB53 when the latter is upregulated by auxin. Altogether, these results indicate that AtHB40 modulates cell division and auxin distribution in the root tip thus altering primary root length and gravitropism.

AtHB23 participates in the gene regulatory network controlling root branching, and reveals differences between secondary and tertiary roots.

In Arabidopsis, lateral root (LR) development is mainly controlled by several known auxin-regulated transcription factors (TFs). Here, we show that AtHB23 (a homeodomain-leucine zipper I TF) participates in this intricate network. Our study of the expression pattern of AtHB23 revealed that it is transcriptionally activated in the early stages of secondary LR primordium (LRP). We found that AtHB23 directly limits the expression of LBD16, a key factor in LR initiation, and also directly induces the auxin transporter gene LAX3. We propose that this HD-Zip I mediates the regulation of LAX3 by ARF7/19. Furthermore, AtHB23 plays distinct roles during the formation of secondary and tertiary roots, exhibiting differential expression patterns. ATHB23 is expressed throughout the tertiary root primordium, whereas it is restricted to early stages in secondary primordia, likely later repressing LBD16 in tertiary LR development and further inhibiting root emergence. Our results suggest that different genetic programs govern the formation of LRP from the main or secondary roots, thereby shaping the global dynamic architecture of the root system.

A uORF Represses the Transcription Factor AtHB1 in Aerial Tissues to Avoid a Deleterious Phenotype.

AtHB1 is an Arabidopsis (Arabidopsis thaliana) homeodomain-leucine zipper transcription factor that participates in hypocotyl elongation under short-day conditions. Here, we show that its expression is posttranscriptionally regulated by an upstream open reading frame (uORF) located in its 5' untranslated region. This uORF encodes a highly conserved peptide (CPuORF) that is present in varied monocot and dicot species. The Arabidopsis uORF and its maize (Zea mays) homolog repressed the translation of the main open reading frame in cis, independent of the sequence of the latter. Published ribosome footprinting results and the analysis of a frame-shifted uORF, in which the repression capability was lost, indicated that the uORF causes ribosome stalling. The regulation exerted by the CPuORF was tissue specific and did not act in the absence of light. Moreover, a photosynthetic signal is needed for the CPuORF action, since plants with uncoupled chloroplasts did not show uORF-dependent repression. Plants transformed with the native AtHB1 promoter driving AtHB1 expression did not show differential phenotypes, whereas those transformed with a construct in which the uORF was mutated exhibited serrated leaves, compact rosettes, and, most significantly, short nondehiscent anthers and siliques containing fewer or no seeds. Thus, we propose that the uncontrolled expression of AtHB1 is deleterious for the plant and, hence, finely repressed by a translational mechanism.

Plant transcription factors from the homeodomain-leucine zipper family I. Role in development and stress responses.

In front of stressful conditions plants display adaptation mechanisms leading to changes in their morphology, physiology, development and molecular composition. Transcription factors (TFs) play crucial roles in these complex adaptation processes. This work is focused in the homeodomain-leucine zipper I (HD-Zip I) family of TFs, unique to plants. First discovered in 1991, they were identified and isolated from monocotyledonous and dicotyledonous plants showing high structural similarity and diversified functions. These TFs have, besides the homeodomain and leucine zipper, conserved motifs in their carboxy-termini allowing the interaction with the basal machinery and with other regulatory proteins. The model dicotyledonous plant Arabidopsis thaliana has 17 HD-Zip I members; most of them regulated by external stimuli and hormones. These TFs are involved in key developmental processes like root and stem elongation, rosette leaves morphology determination, inflorescence stem branching, flowering and pollen hydration. Moreover, they are key players in responses to environmental stresses and illumination conditions. Several HD-Zip I encoding genes from different species were protected in patents because their overexpression or mutation generates improved agronomical phenotypes. Here we discuss many aspects about these TFs including structural features, biological functions and their utilization as biotechnological tools to improve crops. © 2017 IUBMB Life, 69(5):280-289, 2017.

JUNGBRUNNEN1 Confers Drought Tolerance Downstream of the HD-Zip I Transcription Factor AtHB13.

Low water availability is the major environmental factor limiting growth and productivity of plants and crops and is therefore considered of high importance for agriculture affected by climate change. Identifying regulatory components controlling the response and tolerance to drought stress is thus of major importance. The NAC transcription factor (TF) JUNGBRUNNEN1 (JUB1) from Arabidopsis thaliana extends leaf longevity under non-stress growth conditions, lowers cellular hydrogen peroxide (H2O2) level, and enhances tolerance against heat stress and salinity. Here, we additionally find that JUB1 strongly increases tolerance to drought stress in Arabidopsis when expressed from both, a constitutive (CaMV 35S) and an abiotic stress-induced (RD29A) promoter. Employing a yeast one-hybrid screen we identified HD-Zip class I TF AtHB13 as an upstream regulator of JUB1. AtHB13 has previously been reported to act as a positive regulator of drought tolerance. AtHB13 and JUB1 thereby establish a joint drought stress control module.

A matter of quantity: Common features in the drought response of transgenic plants overexpressing HD-Zip I transcription factors.

Plant responses to water deficit involve complex molecular mechanisms in which transcription factors have key roles. Previous reports ectopically overexpressed a few members of the homeodomain-leucine zipper I (HD-Zip I) family of transcription factors from different species, and the obtained transgenic plants exhibited drought tolerance which extent depended on the level of overexpression, triggering diverse molecular and physiological pathways. Here we show that most HD-Zip I genes are regulated by drought in the vegetative and/or reproductive stages. Moreover, uncharacterized members of this family were expressed as transgenes both in Col-0 and rdr6-12 backgrounds and were able to enhance drought tolerance in host plants. The extent of such tolerance depended on the expression level of the transgene and was significantly higher in transgenic rdr6-12 than in Col-0. Comparative transcriptome analyses of Arabidopsis thaliana plants overexpressing HD-Zip I proteins indicated that many members have common targets. Moreover, the water deficit tolerance exhibited by these plants is likely due to the induction and repression of certain of these common HD-Zip I-regulated genes. However, each HD-Zip I member regulates other pathways, which, in some cases, generate differential and potentially undesirable traits in addition to drought tolerance. In conclusion, only a few members of this family could become valuable tools to improve drought-tolerance.

A Predictive Coexpression Network Identifies Novel Genes Controlling the Seed-to-Seedling Phase Transition in Arabidopsis thaliana.

The transition from a quiescent dry seed to an actively growing photoautotrophic seedling is a complex and crucial trait for plant propagation. This study provides a detailed description of global gene expression in seven successive developmental stages of seedling establishment in Arabidopsis (Arabidopsis thaliana). Using the transcriptome signature from these developmental stages, we obtained a coexpression gene network that highlights interactions between known regulators of the seed-to-seedling transition and predicts the functions of uncharacterized genes in seedling establishment. The coexpressed gene data sets together with the transcriptional module indicate biological functions related to seedling establishment. Characterization of the homeodomain leucine zipper I transcription factor AtHB13, which is expressed during the seed-to-seedling transition, demonstrated that this gene regulates some of the network nodes and affects late seedling establishment. Knockout mutants for athb13 showed increased primary root length as compared with wild-type (Columbia-0) seedlings, suggesting that this transcription factor is a negative regulator of early root growth, possibly repressing cell division and/or cell elongation or the length of time that cells elongate. The signal transduction pathways present during the early phases of the seed-to-seedling transition anticipate the control of important events for a vigorous seedling, such as root growth. This study demonstrates that a gene coexpression network together with transcriptional modules can provide insights that are not derived from comparative transcript profiling alone.

Functional characterization of the homeodomain leucine zipper I transcription factor AtHB13 reveals a crucial role in Arabidopsis development.

AtHB13 is a homeodomain leucine zipper I transcription factor whose function in development is largely unknown. AtHB13 and AtHB23 mutant and silenced lines were characterized by expression studies, reciprocal crosses, complementation, molecular analyses, and developmental phenotypes. The athb13-1 and athb13-2 mutants, athb23 silenced, and athb13/athb23 double-silenced plants exhibited faster elongation rates of their inflorescence stems, whereas only athb13-1 and the double-knockdown athb13/athb23 exhibited shorter siliques, fewer seeds, and unfertilized ovules compared with the wild type (WT). The cell sizes of mutant and WT plants were similar, indicating that these transcription factors probably affect cell division. Reciprocal crosses between athb13-1 and the WT genotype indicated that the silique defect was male specific. Pollen hydration assays indicated that the pollen grains of the athb13-1 mutant were unable to germinate on stigmas. AtHB23-silenced plants exhibited normal siliques, whereas double-knockdown athb13/athb23 plants were similar to athb13-1 plants. Both AtHB13 and AtHB23 were able to rescue the abnormal silique phenotype. AtHB23 was upregulated in athb13-2 plants, whereas its transcript levels in athb13-1 mutants were not significantly increased. Transcriptome analysis comparing athb13-1 and WT inflorescences revealed that a large number of genes, including several involved in pollen coat formation, are regulated by AtHB13. Finally, athb13-1 complementation with mutated versions of AtHB13 confirmed that two different tryptophans in its C terminus are essential. We conclude that AtHB13 and AtHB23 play independent, negative developmental roles in stem elongation, whereas only AtHB13 is crucial for pollen germination. Furthermore, AtHB23, which does not normally exert a functional role in pollen, can act as a substitute for AtHB13.

Expression and function of AtMBD4L, the single gene encoding the nuclear DNA glycosylase MBD4L in Arabidopsis.

DNA glycosylases recognize and excise damaged or incorrect bases from DNA initiating the base excision repair (BER) pathway. Methyl-binding domain protein 4 (MBD4) is a member of the HhH-GPD DNA glycosylase superfamily, which has been well studied in mammals but not in plants. Our knowledge on the plant enzyme is limited to the activity of the Arabidopsis recombinant protein MBD4L in vitro. To start evaluating MBD4L in its biological context, we here characterized the structure, expression and effects of its gene, AtMBD4L. Phylogenetic analysis indicated that AtMBD4L belongs to one of the seven families of HhH-GPD DNA glycosylase genes existing in plants, and is unique on its family. Two AtMBD4L transcripts coding for active enzymes were detected in leaves and flowers. Transgenic plants expressing the AtMBD4L:GUS gene confined GUS activity to perivascular leaf tissues (usually adjacent to hydathodes), flowers (anthers at particular stages of development), and the apex of immature siliques. MBD4L-GFP fusion proteins showed nuclear localization in planta. Interestingly, overexpression of the full length MBD4L, but not a truncated enzyme lacking the DNA glycosylase domain, induced the BER gene LIG1 and enhanced tolerance to oxidative stress. These results suggest that endogenous MBD4L acts on particular tissues, is capable of activating BER, and may contribute to repair DNA damage caused by oxidative stress.

Arabidopsis thaliana HomeoBox 1 (AtHB1), a Homedomain-Leucine Zipper I (HD-Zip I) transcription factor, is regulated by PHYTOCHROME-INTERACTING FACTOR 1 to promote hypocotyl elongation.

Arabidopsis thaliana HomeoBox 1 (AtHB1) is a homeodomain-leucine zipper transcription factor described as a transcriptional activator with unknown function. Its role in A. thaliana development was investigated. AtHB1 expression was analyzed in transgenic plants bearing its promoter region fused to reporter genes. Knock-down mutant and overexpressor plant phenotypes were analyzed in different photoperiod regimes. AtHB1 was mainly expressed in hypocotyls and roots and up-regulated in seedlings grown under a short-day photoperiod. AtHB1 knock-down mutants and overexpressors showed shorter and longer hypocotyls, respectively, than wild type (WT). AtHB1 transcript levels were lower in PHYTOCHROME-INTERACTING FACTOR 1 (PIF1) mutants than in controls, suggesting that AtHB1 is regulated by PIF1 in hypocotyls. ß-glucuronidase (GUS) activity in Nicotiana benthamiana leaves cotransformed with PromAtHB1::GUS and 35S::PIF1 indicated that PIF1 induces AtHB1 expression. Hypocotyl lenght was measured in seedlings of athb1, pif1, or double athb1/pif1 mutants and PIF1 or AtHB1 overexpressors in WT, athb1 or pif1 backgrounds, both in short- or long-day. These analyses allowed us to determine that AtHB1 is a factor acting downstream of PIF1. Finally, a transcriptome analysis of athb1 mutant hypocotyls revealed that AtHB1 regulates genes involved in cell wall composition and elongation. The results suggest that AtHB1 acts downstream of PIF1 to promote hypocotyl elongation, especially in response to short-day photoperiods.