Elongation Events Research Articles

Genome-wide association study (GWAS) with high-throughput SNP chip DNA markers identified novel genetic factors for mesocotyl elongation and seedling emergence in rice (Oryza sativa L.) using multiple GAPIT models.

This study employed a joint strategy high-density SNP Chip DNA markers and multiple Genome Association and Prediction Integrated Tool (GAPIT) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), Fixed and random model Circulating Probability Uniform (FarmCPU), General Linear Model (GLM), and Settlement of Mixed Linear Model (MLM) Under Progressively Exclusive Relationship (SUPER)], to investigate novel genetic factors controlling mesocotyl elongation and seedling emergence for direct-seeded rice. Genotype data (230,526 SNP Chip DNA makers) of 117 doubled haploid lines (derived from a cross between 93-11 (Oryza sativa L. ssp. indica) and Milyang352 (O. sativa L. ssp. japonica) were used to perform a Genome-Wide Association Study (GWAS). Results revealed the association between five (5) topmost significant SNP markers, of which number two [AX-155741269, Chr2: 15422406 bp, and AX-155200917, Chr7: 23814085 bp, explaining 37.5% and 13.8% of the phenotypic variance explained (PVE)] are linked to the mesocotyl elongation loci, while three (AX-282097034 and AX-283652873, Chr9: 9882817 bp and 1023383 bp, PVE 64.5%, and 20.2%, respectively, and AX-154356231, Chr1: 17413989 bp, PVE 21.1%) are tightly linked to the loci controlling seedling emergence. The qMEL2-1 and qSEM9-1 are identified as major QTLs explaining 37.5% and 64.5% of the PVE for mesocotyl elongation and seedling emergence, respectively. The AX-282097034 (Chr9: 9882817 bp) was co-detected by four GAPIT models (BLINK, FarmCPU, SUPER, and GLM), while AX-155741269 was co-detected by BLINK and SUPER. Furthermore, a high estimated heritability (Mesocotyl elongation: h2 = 0.955; seedling emergence: h2 = 0.863; shoot length: h2 = 0.707) was observed. Genes harbored by qMEL2-1 and qSEM9-1 have interesting annotated molecular functions that could be investigated through functional studies to uncover their roles during mesocotyl elongation and seedling emergence events in rice. Furthermore, the presence of genes encoding transcription factors, growth- and stress response, or signaling-related genes would suggest that mesocotyl elongation and seedling emergence from deep direct-seeded rice might involve an active signaling cascade and transport of molecules, which could be elucidated through functional analysis. Likewise, genomic selection analysis suggested markers useful for downstream marker-assisted selection (MAS).

Waterlogging restricted cotton fiber elongation by reducing osmolyte accumulation and cell wall biosynthesis

Waterlogging severely threatens the formation of cotton fiber quality, especially the length. However, the underlying mechanism is still incompletely understood. Here, the experiment (control: soil relative water content at (75 ± 5)%; treatment: waterlogging for 6 days) was conducted during the flowering and boll forming stage using two upland cotton cultivars (Dexiamian 1 and Yuzaomian 9110) to investigate the effects of waterlogging on fiber development from both transcriptomic and physiological levels. The transcriptome analysis of 10 days post anthesis cotton fiber showed that waterlogging significantly regulated the expression of genes associated with fiber elongation events including osmotic solutes accumulation, fiber cell wall biosynthesis, and cell wall remodeling and loosening. Waterlogging decreased the sucrose input into cotton fiber, resulting in reduced sucrose and hexose contents. Under waterlogging, the accumulation of malate and K+ in both cultivars was reduced by decreasing phosphoenolpyruvate carboxylase (PEPC) activity and potassium transporter genes (GhPOT) expression, respectively. Thus, the total concentration of osmolytes was reduced, which dampened cotton fiber elongation. Due to reduced sucrose synthase activity and uridine diphosphate glucose content, the cellulose biosynthesis was limited, leading to decreased fiber cell wall accumulation, which was adverse to fiber elongation. Besides, genes responsible for cell wall remodeling and loosening, including xyloglucan endotransglucosylase/hydrolase genes (GhXTH), α-expansin genes (GhEXPA), and pectin methylesterase genes (GhPME) were also responsive to waterlogging, but in different ways between cultivars. Overall, the shortened cotton fiber could be attributed to reduced osmolytes accumulation and cell wall biosynthesis, whilst the effects of waterlogging on cotton fiber cell wall loosening require further exploration.

Mimicking the last step of gene elongation: hints from the bacterial hisF gene

Gene elongation consists in an in-tandem duplication of a gene and divergence and fusion of the two copies, resulting in a gene constituted by two divergent paralogous modules. Many present-day proteins show internal repeats of amino acid sequences, generated by gene elongation events; however, gene elongation is still a poorly studied evolutionary molecular mechanism. The most documented case is that of the histidine biosynthetic genes hisA and hisF, which derive from the gene elongation of an ancestral gene half the size of the extant ones.The aim of this work was to experimentally simulate the possible last step of the gene elongation event occurred during hisF gene evolution under selective pressure conditions.Azospirillum brasilense hisF gene, carrying a single nucleotide mutation that generates a stop codon between the two halves of the gene, was used to transform the histidine-auxotrophic Escherichia coli strain FB182 (hisF892). The transformed strain was subjected to selective pressure (i.e., low concentration/absence of histidine in the growth medium) and the obtained mutants were characterized.The restoration of prototrophy was strongly dependent on the time of incubation and on the strength of the selective pressure. The mutations involved the introduced stop codon with a single base substitution and none of the mutants restored the wild-type codon. Possible correlations between the different mutations and i) E. coli codon usage, ii) three-dimensional structures of the mutated HisF proteins, and iii) growth ability of the mutants were investigated. On the contrary, when the experiment was repeated by mutating a more conserved codon, only a synonymous substitution was obtained.Thus, experiments performed in this study allowed to mimic a possible gene elongation event occurred during the evolution of hisF gene, evidencing the ability of bacterial cells to modify their genome in short times under selective conditions.

Indoloquinoline-Mediated Targeted Downregulation of KRAS through Selective Stabilization of the Mid-Promoter G-Quadruplex Structure.

KRAS is a well-validated anti-cancer therapeutic target, whose transcriptional downregulation has been demonstrated to be lethal to tumor cells with aberrant KRAS signaling. G-quadruplexes (G4s) are non-canonical nucleic acid structures that mediate central dogmatic events, such as DNA repair, telomere elongation, transcription and splicing events. G4s are attractive drug targets, as they are more globular than B-DNA, enabling more selective gene interactions. Moreover, their genomic prevalence is increased in oncogenic promoters, their formation is increased in human cancers, and they can be modulated with small molecules or targeted nucleic acids. The putative formation of multiple G4s has been described in the literature, but compounds with selectivity among these structures have not yet been able to distinguish between the biological contribution of the predominant structures. Using cell free screening techniques, synthesis of novel indoloquinoline compounds and cellular models of KRAS-dependent cancer cells, we describe compounds that choose between KRAS promoter G4near and G4mid, correlate compound cytotoxic activity with KRAS regulation, and highlight G4mid as the lead molecular non-canonical structure for further targeting efforts.

Peptidyl transferase center decompaction and structural constraints during early protein elongation on the ribosome

Peptide bond formation on the ribosome requires that aminoacyl-tRNAs and peptidyl-tRNAs are properly positioned on the A site and the P site of the peptidyl transferase center (PTC) so that nucleophilic attack can occur. Here we analyse some constraints associated with the induced-fit mechanism of the PTC, that promotes this positioning through a compaction around the aminoacyl ester orchestrated by U2506. The physical basis of PTC decompaction, that allows the elongated peptidyl-tRNA to free itself from that state and move to the P site of the PTC, is still unclear. From thermodynamics considerations and an analysis of published ribosome structures, the present work highlights the rational of this mechanism, in which the free-energy released by the new peptide bond is used to kick U2506 away from the reaction center. Furthermore, we show the evidence that decompaction is impaired when the nascent peptide is not yet anchored inside the exit tunnel, which may contribute to explain why the first rounds of elongation are inefficient, an issue that has attracted much interest for about two decades. Results in this field are examined in the light of the present analysis and a physico-chemical correlation in the genetic code, which suggest that elementary constraints associated with the size of the side-chain of the amino acids penalize early elongation events.

The Library Derived 4554W Peptide Inhibits Primary Nucleation of α-Synuclein

Aggregation of α-Synuclein (αS) is widely regarded as a key factor in neuronal cell death, leading to a wide range of synucleinopathies, including Parkinson’s Disease. Development of therapeutics has therefore focused on inhibiting aggregation of αS into toxic forms. One such inhibitor, based on the preNAC region αS45-54 (4554W), was identified using an intracellular peptide library screen, and subsequently shown to both inhibit formation of αS aggregates while simultaneously lowering toxicity. Subsequent efforts have sought to determine the mode of 4554W action. In particular, and consistent with the fact that both target and peptide are co-produced during library screening, we find that the peptide inhibits primary nucleation of αS, but does not modulate downstream elongation or secondary nucleation events. These findings hold significant promise towards mechanistic understanding and development of molecules that can module the first steps in αS aggregation towards novel treatments for Parkinson’s disease and related synucleinopathies.

Human shelterin protein POT1 prevents severe telomere instability induced by homology-directed DNA repair.

The evolutionarily conserved POT1 protein binds single-stranded G-rich telomeric DNA and has been implicated in contributing to telomeric DNA maintenance and the suppression of DNA damage checkpoint signaling. Here, we explore human POT1 function through genetics and proteomics, discovering that a complete absence of POT1 leads to severe telomere maintenance defects that had not been anticipated from previous depletion studies in human cells. Conditional deletion of POT1 in HEK293E cells gives rise to rapid telomere elongation and length heterogeneity, branched telomeric DNA structures, telomeric R-loops, and telomere fragility. We determine the telomeric proteome upon POT1-loss, implementing an improved telomeric chromatin isolation protocol. We identify a large set of proteins involved in nucleic acid metabolism that engage with telomeres upon POT1-loss. Inactivation of the homology-directed repair machinery suppresses POT1-loss-mediated telomeric DNA defects. Our results unravel as major function of human POT1 the suppression of telomere instability induced by homology-directed repair.

Theory of transcription bursting: stochasticity in the transcription rates

Transcription bursting creates variation among the individuals of a given population. Bursting emerges as the consequence of turning on and off the transcription process randomly. There are at least three sub-processes involved in the bursting phenomenon with different timescale regimes viz. flipping across the on–off state channels, microscopic transcription elongation events and the mesoscopic transcription dynamics along with the mRNA recycling. We demonstrate that when the flipping dynamics is coupled with the microscopic elongation events, then the distribution of the resultant transcription rates will be over-dispersed. This in turn reflects as the transcription bursting with over-dispersed non-Poisson type distribution of mRNA numbers. We further show that there exist optimum flipping rates (αC, βC) at which the stationary state Fano factor and variance associated with the mRNA numbers attain maxima. These optimum points are connected via $$ \alpha_{C} = \sqrt {\beta_{C} \left( {\beta_{C} + \gamma_{r} } \right)} $$ . Here α is the rate of flipping from the on-state to the off-state, β is the rate of flipping from the off-state to the on-state and γr is the decay rate of mRNA. When α = β = χ with zero rate in the off-state channel, then there exist optimum flipping rates at which the non-stationary Fano factor and variance attain maxima. Here $$ \chi_{C,v} \simeq {{3k_{r}^{ + } } \mathord{\left/ {\vphantom {{3k_{r}^{ + } } {2\left( {1 + k_{r}^{ + } t} \right)}}} \right. \kern-0pt} {2\left( {1 + k_{r}^{ + } t} \right)}} $$ (here $$ k_{r}^{ + } $$ is the rate of transcription purely through the on-state elongation channel) is the optimum flipping rate at which the variance of mRNA attains a maximum and $$ \chi_{C,\kappa } \simeq {{1.72} \mathord{\left/ {\vphantom {{1.72} t}} \right. \kern-0pt} t} $$ is the optimum flipping rate at which the Fano factor attains a maximum. Close observation of the transcription mechanism reveals that the RNA polymerase performs several rounds of stall-continue type dynamics before generating a complete mRNA. Based on this observation, we model the transcription event as a stochastic trajectory of the transcription machinery across these on–off state elongation channels. Each mRNA transcript follows different trajectory. The total time taken by a given trajectory is the first passage time (FPT). Inverse of this FPT is the resultant transcription rate associated with the particular mRNA. Therefore, the time required to generate a given mRNA transcript will be a random variable. For a stall-continue type dynamics of RNA polymerase, we show that the overall average transcription rate can be expressed as $$ k_{r} \simeq h_{\infty }^{ + } k_{r}^{ + } $$ where $$ k_{r}^{ + } \simeq {{\lambda_{r}^{ + } } \mathord{\left/ {\vphantom {{\lambda_{r}^{ + } } L}} \right. \kern-0pt} L} $$ , λ+ is the microscopic transcription elongation rate in the on-state channel and L is the length of a complete mRNA transcript and h∞+ = [β/(α + β)] is the stationary state probability of finding the transcription machinery in the on-state channel.

The Role of Gene Elongation in the Evolution of Histidine Biosynthetic Genes.

Gene elongation is a molecular mechanism consisting of an in-tandem duplication of a gene and divergence and fusion of the two copies, resulting in a gene constituted by two divergent paralogous modules. The aim of this work was to evaluate the importance of gene elongation in the evolution of histidine biosynthetic genes and to propose a possible evolutionary model for some of them. Concerning the genes hisA and hisF, which code for two homologous (β/α)8-barrels, it has been proposed that the two extant genes could be the result of a cascade of gene elongation/domain shuffling events starting from an ancestor gene coding for just one (β/α) module. A gene elongation event has also been proposed for the evolution of hisB and hisD; structural analyses revealed the possibility of an early elongation event, resulting in the repetition of modules. Furthermore, it is quite possible that the gene elongations responsible for the evolution of the four proteins occurred before the earliest phylogenetic divergence. In conclusion, gene elongation events seem to have played a crucial role in the evolution of the histidine biosynthetic pathway, and they may have shaped the structures of many genes during the first steps of their evolution.

A New Microengineered Platform for 4D Tracking of Single Cells in a Stem-Cell-Based In Vitro Morphogenesis Model.

Recently developed stem-cell-based in vitro models of morphogenesis can help shed light on the mechanisms involved in embryonic patterning. These models are showcased using traditional cell culture platforms and materials, which allow limited control over the biological system and usually do not support high-content imaging. In contrast, using advanced microengineered tools can help in microscale control, long-term culture, and real-time data acquisition from such biological models and aid in elucidating the underlying mechanisms. Here, a new culturing, manipulation and analysis platform is described to study in vitro morphogenesis using thin polycarbonate film-based microdevices. A pipeline consisting of open-source software to quantify 3D cell movement using 4D image acquisition is developed to analyze cell migration within the multicellular clusters. It is shown that the platform can be used to control and study morphogenesis in non-adherent cultures of the P19C5 mouse stem cell line and mouse embryonic stem cells (mESCs) that show symmetry breaking and axial elongation events similar to early embryonic development. Using the new platform, it is found that localized cell proliferation and coordinated cell migration result in elongation morphogenesis of the P19C5 aggregates. Further, it is found that polarization and elongation of mESC aggregates are dependent on directed cell migration.

The structural basis for intermitochondrial communications is fundamentally different in cardiac and skeletal muscle.

What is the topic for this review? This review summarizes recent discoveries in mitochondrial development and morphology studied with electron microscopy. What advances does it highlight? Although mitochondria are generally considered to be isolated from each other, this review highlights recently discovered evidence for the presence of intermitochondrial communication structures in cardiac and skeletal muscle, in animal models and humans. Within striated muscles, the means of intermitochondrial exchange and the reaction of mitochondria to external stimuli are uniquely dependent on the tissue, and we clearly differentiate between nanotunnels, the active protrusion of cardiac mitochondria, and the connecting ducts of skeletal muscle derived from fusion-fission and elongation events. This review focuses on recent discoveries in skeletal and cardiac muscles indicating that mitochondria behave as an interactive cohort with inter-organelle communication and specific reactions to stress signals. Our new finding is that intermitochondrial communications in cardiac and skeletal muscles rely on two distinct methods. In cardiac muscle, mitochondria are discrete entities and are fairly well immobilized in a structural context. The organelles have developed a unique method of communication, via nanotunnels, which allow temporary connection from one mitochondrion to another over distances of up to several micrometres, without overall movement of the individual organelles and loss of their identity. Skeletal muscle mitochondria, in contrast, are dynamic. Through fusion, fission and elongation, they form connections that include constrictions and connecting ducts (distinct from nanotunnels) and lose individual identity in the formation of extensive networks. Connecting elements in skeletal muscle are distinct from nanotunnels in cardiac muscle.

Multifunctional Stretchable Conductive Woven Fabric Containing Metal Wire with Durable Structural Stability and Electromagnetic Shielding in the X-Band.

Elastomeric, conductive composite yarns have recently received attention around the opportunity for them to offer special protective fields. A straightforward approach for fabricating tri-component elastic-conductive composite yarns (t-ECCYs) containing stainless steel wire (SSW) was proposed previously. This work mainly focuses on the electromagnetic shielding effectiveness (EMSE) of weft-stretchable woven fabric containing t-ECCY over the X-band under different testing conditions, e.g., single step-by-step elongation, cyclic stretch and lamination events. Results showed that a woven cotton fabric with weft yarn of t-ECCY not only exhibited superior weft stretch-ability to a higher elongation (>40%) compared with a pure cotton control but also had an acceptable 15-cyclic stability with 80% shape recovery retention. The t-ECCY weft fabric was effective in shielding electromagnetic radiation, and its EMSE was also enhanced at elevated elongations during stretch at parallel polarization of EM waves. There was also no decay in EMSE before and after the t-ECCY fabric was subject to 15 stretch cycles at extension of 20%. In addition, a 90° by 90° cross lamination of t-ECCY fabric remarkably improved the EMSE compared to a 0°/90° one. The scalable fabrication strategy and excellent EMSE seen in t-ECCY-incorporated fabrics represent a significant step forward in protective fields.

A short translational ramp determines the efficiency of protein synthesis

Translation initiation is a major rate-limiting step for protein synthesis. However, recent studies strongly suggest that the efficiency of protein synthesis is additionally regulated by multiple factors that impact the elongation phase. To assess the influence of early elongation on protein synthesis, we employed a library of more than 250,000 reporters combined with in vitro and in vivo protein expression assays. Here we report that the identity of the amino acids encoded by codons 3 to 5 impact protein yield. This effect is independent of tRNA abundance, translation initiation efficiency, or overall mRNA structure. Single-molecule measurements of translation kinetics revealed pausing of the ribosome and aborted protein synthesis on codons 4 and 5 of distinct amino acid and nucleotide compositions. Finally, introduction of preferred sequence motifs only at specific codon positions improves protein synthesis efficiency for recombinant proteins. Collectively, our data underscore the critical role of early elongation events in translational control of gene expression.

SETD2 reduction adversely affects the development of mouse early embryos.

SET domain-containing protein 2 (SETD2), the protein of regulating trimethylation status of histone H3 at lysine 36 (H3K36), participates in the maintenance of chromatin architecture, transcription elongation, genome stability, and other biological events. However, its function in preimplantation embryos is still obscure. In this study, specific small interfering RNA was employed to investigate the functions of SETD2. We find that deletion of SETD2 results in the developmental delay of mouse early embryos, indicative of the compromised developmental potential. Remarkably, SETD2 knockdown induces the accumulation of the DNA lesions and apoptotic blastomeres in early embryos. In addition, the methylation level of H3K36 is significantly reduced in two-cell embryos depleted of SETD2. In summary, our data indicate that SETD2 maintains genome stability perhaps via regulating trimethylation status of H3K36, consequently controlling the embryo quality. These findings pave the avenue for understanding the cross-talk between epigenome and SETD2 during early embryo development.

In Toto Imaging of Dynamic Osteoblast Behaviors in Regenerating Skeletal Bone

Osteoblasts are matrix-depositing cells that can divide and heal bone injuries. Their deep-tissue location and the slow progression of bone regeneration challenge attempts to capture osteoblast behaviors in live tissue at high spatiotemporal resolution. Here, we have developed an imaging platform to monitor and quantify individual and collective behaviors of osteoblasts in adult zebrafish scales, skeletal body armor discs that regenerate rapidly after loss. Using a panel of transgenic lines that visualize and manipulate osteoblasts, we find that a founder pool of osteoblasts emerges through de novo differentiation within one day of scale plucking. These osteoblasts undergo division events that are largely uniform in frequency and orientation to establish aprimordium. Osteoblast proliferation dynamics diversify across the primordium by two days after injury, with cell divisions focused near, and with orientations parallel to, the scale periphery, occurring coincident with dynamic localization of fgf20a gene expression. In posterior scale regions, cell elongation events initiate in areas soon occupied by mineralized grooves called radii, beginning approximately 2days post injury, with patterned osteoblast death events accompanying maturation of these radii. By imaging at single-cell resolution, we detail acquisition of spatiotemporally distinct cell division, motility, and death dynamics within a founder osteoblast pool as bone regenerates.

Crystal structure of human Mediator subunit MED23

The Mediator complex transduces regulatory information from enhancers to promoters and performs essential roles in the initiation of transcription in eukaryotes. Human Mediator comprises 26 subunits forming three modules termed Head, Middle and Tail. Here we present the 2.8 Å crystal structure of MED23, the largest subunit from the human Tail module. The structure identifies 25 HEAT repeats-like motifs organized into 5 α-solenoids. MED23 adopts an arch-shaped conformation, with an N-terminal domain (Nter) protruding from a large core region. In the core four solenoids, motifs wrap on themselves, creating triangular-shaped structural motifs on both faces of the arch, with extended grooves propagating through the interfaces between the solenoid motifs. MED23 is known to interact with several specific transcription activators and is involved in splicing, elongation, and post-transcriptional events. The structure rationalizes previous biochemical observations and paves the way for improved understanding of the cross-talk between Mediator and transcriptional activators.

Investigation on the Evolutionary Relation of Diverse Polyhydroxyalkanoate Gene Clusters in Betaproteobacteria.

Products of numerous genes (phaC, phaA, phaB, phaP, phaR, and phaZ) are involved in the synthesis and degradation processes of the ubiquitous prokaryotic polyhydroxyalkanoate (PHA) intracellular reserve storage system. In this study, we performed a bioinformatics analysis to identify PHA-related genes and proteins in the genome of 66 selected organisms (class: Betaproteobacteria) that occur in various habitats; besides, evolutionary trajectories of the PHA system are reported here. The identified PHA-related genes were organized into clusters, and the gene arrangement was highly diverse. The occurrence and distribution of PHA-related clusters revealed that a single cluster was primarily segmented into small gene groups among various genomes, which were further reorganized as novel clusters based on various functional genes. The individual phylogenies of gene and protein sequences supported that the clusters were assembled through the relocation of native orthologous genes that underwent insertion, deletion, and elongation events. Furthermore, the neighboring genes provided valuable evolutionary and functional cues regarding the conservation and maintenance of PHA-related genes in the genome. Overall, the aforementioned results strongly indicate the influence of horizontal gene transfer on the organization of PHA-related gene clusters. Therefore, our results reveal new insights into the organization, evolutionary history, and cluster conservation of the PHA-related gene inventories among Betaproteobacterial organisms.

Viscoelastic Dissipation Stabilizes Cell Shape Changes during Tissue Morphogenesis

Tissue morphogenesis relies on the production ofactive cellular forces. Understanding how such forces are mechanically converted into cell shape changes is essential to our understanding of morphogenesis. Here, we use myosin II pulsatile activity during Drosophila embryogenesis to study how transient forces generate irreversible cell shape changes. Analyzing the dynamics of junction shortening and elongation resulting from myosin II pulses, we find that long pulses yield less reversible deformations, typically a signature of dissipative mechanics. This is consistent with a simple viscoelastic description, which we use to model individual shortening and elongation events. The model predicts that dissipation typically occurs on the minute timescale, a timescale commensurate with that of force generation by myosin II pulses. We test this estimate by applying time-controlled forces on junctions with optical tweezers. Finally, we show that actin turnover participates in dissipation, as reducing it pharmacologically increases the reversibility of contractile events. Our results argue that active junctional deformation is stabilized by actin-dependent dissipation. Hence, tissue morphogenesis requires coordination between force generation and dissipation.

Splicing and transcription touch base: co-transcriptional spliceosome assembly and function

Several macromolecular machines collaborate to produce eukaryotic messenger RNA. RNA polymerase II (Pol II) translocates along genes that are up to millions of base pairs in length and generates a flexible RNA copy of the DNA template. This nascent RNA harbours introns that are removed by the spliceosome, which is a megadalton ribonucleoprotein complex that positions the distant ends of the intron into its catalytic centre. Emerging evidence that the catalytic spliceosome is physically close to Pol II in vivo implies that transcription and splicing occur on similar timescales and that the transcription and splicing machineries may be spatially constrained. In this Review, we discuss aspects of spliceosome assembly, transcription elongation and other co-transcriptional events that allow the temporal coordination of co-transcriptional splicing.

Distribution of some pectic and arabinogalactan protein epitopes during Solanum lycopersicum (L.) adventitious root development

BackgroundThe adventitious roots (AR) of plants share the same function as primary and lateral roots (LR), although their development is mainly an adaptive reaction to stress conditions. Regeneration of grafted plants is often accompanied by AR formation thus making the grafting technique a good model for studying AR initiation and development and their means of emergence. Pectins and arabinogalactan proteins (AGP) are helpful markers of particular cellular events, such as programmed cell death (PCD), elongation, proliferation or other differentiation events that accompany AR development. However, little is known about the distribution of pectins and AGPs during AR ontogeny, either in the primordium or stem tissues from which AR arise or their correspondence with these events during LR formation.ResultsAR were developed from different stem tissues such as parenchyma, xylem rays and the cambium, depending on the stem age and treatment (grafting versus cutting) of the parental tissue. Immunochemical analysis of the presence of pectic (LM8, LM19, LM20) and AGP (JIM8, JIM13, JIM16) epitopes in AR and AR-associated tissues showed differential, tissue-specific distributions of these epitopes. Two pectic epitopes (LM19, LM20) were developmentally regulated and the occurrence of the LM8 xylogalacturonan epitope in the root cap of the AR differed from other species described so far. AGP epitopes were abundantly present in the cytoplasmic compartments (mainly the tonoplast) and were correlated with the degree of cell vacuolisation. JIM8 and JIM13 epitopes were detected in the more advanced stages of primordium development, whereas the JIM16 epitope was present from the earliest division events of the initial AR cells. The comparison between AR and LR showed quantitative (AGP,) and qualitative (pectins) differences.ConclusionThe chemical compositions of adventitious and lateral root cells show differences that correlate with the different origins of these cells. In AR, developmental changes in the distribution of pectins and AGP suggest the turnover of wall compounds. Our data extend the knowledge about the distribution of pectin and AGP during non-embryogenic root development in a species that is important from an agronomic point of view.