Intact Arabidopsis RPB1 functions in stem cell niches maintenance and cell cycling control

RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize

Maize (Zea mays) kernel size is an important factor determining grain yield; although numerous genes regulate kernel development, the roles of RNA polymerases in this process are largely unclear. Here, we characterized the defective kernel 701 (dek701) mutant that displays delayed endosperm development but normal vegetative growth and flowering transition, compared to its wild type. We cloned Dek701, which encoded ZmRPABC5b, a common subunit to RNA polymerases I, II and III. Loss-of-function mutation of Dek701 impaired the function of all three RNA polymerases and altered the transcription of genes related to RNA biosynthesis, phytohormone response and starch accumulation. Consistent with this observation, loss-of-function mutation of Dek701 affected cell proliferation and phytohormone homeostasis in maize endosperm. Dek701 was transcriptionally regulated in the endosperm by the transcription factor Opaque2 through binding to the GCN4 motif within the Dek701 promoter, which was subjected to strong artificial selection during maize domestication. Further investigation revealed that DEK701 interacts with the other common RNA polymerase subunit ZmRPABC2. The results of this study provide substantial insight into the Opaque2-ZmRPABC5b transcriptional regulatory network as a central hub for regulating endosperm development in maize.

The RNA polymerase II subunit NRPB2 is required for indeterminate root development, cell viability, stem cell niche maintenance, and de novo root tip regeneration in Arabidopsis

The RNA polymerase II drives the biogenesis of coding and non-coding RNAs for gene expression. Here, we describe new roles for its second-largest subunit, NRPB2, on root organogenesis and regeneration. Down-regulation of NRPB2 activates a determinate developmental program, which correlated with a reduction in mitotic activity, cell elongation, and size of the root apical meristem. Noteworthy, nrpb2-3 mutants manifest cell death in pro-vascular cells within primary root tips of plants grown in darkness or exposed to light, which triggers the expression of the regeneration gene marker ERF115 in neighbor cells close to damage. Auxin and stem cell niche (SCN) gene expression as well as structural analysis revealed that NRPB2 maintains SCN activity through distribution of PIN transporters in root tissues. Wild-type seedlings regenerated the root tip after excision of the QC and SCN, but nrpb2-3 mutants did not rebuild the missing tissues, and this process could be genotypified using pERF115:GFP, DR5:GFP, and pWOX5:GFP reporter constructs. The levels of reactive oxygen species increased in the mutants four days after germination and strongly decreased at later times, whereas nitric oxide accumulated as the root tip differentiates. These results show the importance of the transcriptional machinery for root organogenesis, cell viability, and regenerative capacity for reconstruction of tissues and organs upon injury.

De novo POLR2A p.(Ile457Thr) variant associated with early-onset encephalopathy and cerebellar atrophy: expanding the phenotypic spectrum

BACKGROUND

Heterozygous POLR2A variants have been recently reported in patients with a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia. POLR2A encodes the highly conserved RBP1 protein, an essential subunit of the DNA-dependent RNA polymerase II.

CASE PRESENTATION

We investigated a 12-year-old girl presenting with an early-onset encephalopathy characterized by psychomotor delay, facial dysmorphism, refractory epilepsy with variable seizure types, behavioural abnormalities, and sleep disorder. Brain MRI showed a slowly progressive cerebellar atrophy. Trio-exome sequencing (Trio-ES) revealed the de novo germline variant NM_000937.5:c.1370T>C; p.(Ile457Thr) in POLR2A. This variant was previously reported in a subject with profound generalized hypotonia and muscular atrophy by Haijes et al. Our patient displayed instead a severe epileptic phenotype with refractory hypotonic seizures with impaired consciousness, myoclonic jerks, and drop attacks.

CONCLUSION

This case expands the clinical spectrum of POLR2A-related syndrome, highlighting its phenotypic variability and supporting the relevance of epilepsy as a core feature of this emerging condition.

Serine Hydroxymethyltransferase 1 Is Essential for Primary-Root Growth at Low-Sucrose Conditions

Plant roots are essential organs for absorbing nutrients from the soil or medium. Sucrose functions as a vital carbon source in root development, and sucrose starvation interferes with the redox state of plant cells. However, the mechanism of root growth at sucrose starvation remains unclear. Here, we report that SHMT1 (serine hydroxymethyltransferase 1) plays a crucial role in primary-root growth. SHMT1 mutation caused decreased sugar levels, excessive H₂O₂ accumulation, and severe root-growth arrest at sucrose-free conditions, whereas plants with SHMT1 overexpression had increased sugar and decreased H₂O₂ levels, and longer primary roots. Sucrose supply fully restored root growth of shm1-2, but CO₂ alone could not, and SHMT1 is much more stable in roots than shoots at sucrose conditions, suggesting that SHMT1 accumulation in roots is critical for sucrose accumulation and root growth. Further ROS scavenging by GSH application or ROS synthesis inhibition by apocynin application or RBOHD mutation reduced H₂O₂ levels and partially restored the root-growth arrest phenotype of shm1-2 at low-sucrose conditions, suggesting that SHMT1 modulates root growth via sucrose-mediated ROS accumulation. Our findings demonstrated the role of SHMT1 in primary-root growth by regulating sucrose accumulation and ROS homeostasis in roots.

RAB GTPASE HOMOLOG 8D is required for the maintenance of both the root stem cell niche and the meristem

Previous studies have suggested that the plastid translation elongation factor, elongation factor thermo unstable (EF-Tu), encoded by RAB GTPASE HOMOLOG 8D (RAB8D) is essential for plant growth. Here, through analyzing the root phenotypes of two knock-down alleles of RAB8D (rab8d-1 and rab8d-2), we further revealed a vital role for RAB8D in primary root development through the maintenance of both the stem cell niche (SCN) and the meristem. Our results showed that RAB8D deficiency affects the root auxin response and SCN maintenance signaling. RAB8D interacts with GENOMES UNCOUPLED 1 (GUN1) in vivo. Further analysis revealed that GUN1 is over-accumulated and is required for both stem cell death and maintenance of root architecture in rab8d Arabidopsis mutants. The ATAXIA-TELANGIECTASIA-MUTATED (ATM)-SUPPRESSOR OF GAMMA RESPONSE 1 pathway is involved in the regulation of root meristem size through upregulating SIAMESE-RELATED 5 expression in the rab8d-2 allele. Moreover, ETHYLENE RESPONSE FACTOR 115 is highly expressed in rab8d-2, which plays a role in further quiescent center division. Our observations not only characterized the role of RAB8D in root development, but also uncovered functions of GUN1 and ATM in response to plastid EF-Tu deficiency.

Trichostatin A and sodium butyrate promotes plant regeneration in common wheat

Histone acetylation modification plays a vital role in plant cell division and differentiation. However, the function on wheat mature embryo culture has not been reported. Here, we used the mature embryo of wheat genotypes including CB037, Fielder, and Chinese Spring (CS) as materials to analyze the effects of different concentrations of trichostatin A (TSA) and sodium butyrate (SB) on plant regeneration efficiency. The results showed that, compared with the control group, the induction rates of embryogenic callus and green shoot were significantly increased with the addition of 0.5 µM TSA, while they were reduced under treatment of 2.5 µM TSA on wheat mature embryo. With the respective addition of 200 µM and 1000 µM SB, regeneration frequency of three genotypes was enhanced, especially in Fielder, which reached significant difference compared with the control group. Unfortunately, 0.5 µM TSA and 200 µM SB combination had no apparent effect on wheat regeneration frequency. The results indicated that TSA and SB increase plant regeneration in common wheat. In addition, TSA had a common effect and SB had different effect among genotypes on wheat regeneration frequency. The mechanism of action needs further investigation.

Determinate root development in the halted primary root1 mutant of Arabidopsis correlates with death of root initial cells and an enhanced auxin response

The transit from indeterminate to determinate root developmental program compromises growth and causes the differentiation of the meristem, but a direct link between this process with auxin signaling and/or viability of initial cells remains untested. Here, through the isolation and characterization of the halted primary root1 (hpr1) mutant of Arabidopsis, which develops primary and lateral roots with genetically stable determinate growth after germination, we show that the differentiation of the root meristem correlates with enhanced auxin responsiveness and is preceded by the death of provasculature initial cells in both primary and lateral roots. Supplementation of indole-3-acetic acid causes both a dose-dependent repression of primary root growth and an induction of DR5:uidA expression in wild-type seedlings, and these effects were exacerbated in hpr1 mutants. The damage of provasculature initial cells in the root of hpr1 mutants occurred at earlier times than the full differentiation of the meristem, and correlates with a reduced expression domain of CycB1:uidA and PRZ:uidA. Thus, HPR1 plays critical functions for stem cell maintenance, auxin homeostasis, cell division in the meristem, and indeterminate root growth.

De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia

The RNA polymerase II complex (pol II) is responsible for transcription of all ∼21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly disease-causing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.

Young seedlings adapt to stress by retaining starch and retarding growth through ABA-Dependent and -independent pathways in Arabidopsis

The metabolism of starch, the major resource of carbohydrates and an essential determinant of plant fitness in plants, often exhibits plasticity in response to challenging environmental conditions. Previous study of leaf starch turnover under abiotic stresses documented conflicting patterns. To understand this discrepancy and examine the process in more detail, we grew Arabidopsis seedlings under a series of typical stress conditions, observed and quantified leaf starch content at different time. By electron microscope, iodine staining and starch quantification, we confirm that short-term (<8 h) stress treatments, such as osmotic stress, high salinity, caused rapid starch decrease during the night while long-term (>56 h) stresses increased starch content significantly. Exogenous abscisic acid (ABA) induced similar effects to the abiotic stresses. Comparison of the starch content in wild type (WT) and the ABA receptor quadruple mutant pyr1;pyl1;pyl2;pyl4 suggests that the stress-induced starch turnover change is also mediated by ABA-independent pathways. In addition, more energy supply caused severer growth defect under stress conditions. And the transcription levels of both starch biosynthesis enzymes (APL1 and APL3) and starch degradation enzymes (SEX1, SEX4, BAM1 and BAM3) exhibited differential increase under long-term stresses. Taken together, our data strongly suggest that young seedlings adapt to stress by retaining starch and retarding growth through both ABA-dependent and -independent pathways.

Arabidopsis IAR4 Modulates Primary Root Growth Under Salt Stress Through ROS-Mediated Modulation of Auxin Distribution

High salinity is one of the major environmental stresses that plants encounter. Roots are the initial and direct organs to perceive the signal. However, how plant roots perceive and respond to salinity at the molecular and physiological levels is still poorly understood. Here, we report that IAA-CONJUGATE-RESISTANT 4 (IAR4) plays a key role in primary root growth under salt stress conditions. Mutation of IAR4 led to increased sensitivity to salt stress conditions, with strongly inhibited primary root growth and reduced survival rate in two iar4 mutant alleles. iar4 mutants accumulated greater Na⁺ and exhibited a greater Na⁺/K⁺ ratio under NaCl treatment. In addition, more reactive oxygen species (ROS) accumulated in the iar4 mutants due to reduced ROS scavenging. NaCl treatment greatly suppressed the expression levels of ProPIN1:PIN1-GFP, ProPIN2:PIN2-GFP, ProPIN3:PIN3-GFP, and ProDR5:GFP, and suppressed root meristem activity in iar4. GSH or auxin treatment greatly recovered the PIN expression, auxin distribution and primary root growth in the iar4 mutants, suggesting ROS is a vital mediator between salt stress and auxin response. Our data support a model in which IAR4 integrates ROS and auxin pathways to modulate primary root growth under salinity stress conditions, by regulation of PIN-mediated auxin transport.

Full-length RPB1 is required in two-step shoot regeneration

Regeneration is a complicated progress in plants and animals. Most multicellular organisms can regenerate new tissue when wounded, and plants excel most animals in their ability to regenerate whole new growth module from adult tissues. Regeneration in Arabidopsis includes two steps. Firstly, the explants from differentiated plant tissues such as roots or hypocotyls are induced to generate callus, then the shoots regenerate upon the callus. The phytohormone auxin and cytokinin play important parts in this process. And genes related to auxin and cytokinin siganls involved in the regeneration have been studied widely. As we reported before, in Arabidopsis the full-length CTD of RNA Polymerase II's largest subunit RPB1 is necessary in keeping normal cell cycling and maintaining stem cell niches. Here, we report that the mutants of card1s have significant defects in the regeneration progress both in the induction of callus and the formation of shoot. All the results further proved the importance of intact RPB1 from a distinctive perspective.