Biology subjects

Chotewutmontri, P.

Publications and source records attributed to Chotewutmontri, P..

9 recordsLinked to original sources

bioRxiv2026

Chromosomal rearrangements 1 and sequence similarity drivepreferential allosyndetic introgression from a wild relative into wheat

Recombination in polyploid genomes is generally constrained to homologous or homoeologous chromosomes; however, how chromosomal rearrangements influence recombination between chromosomes remains unclear. Here, we demonstrate that large-scale chromosomal rearrangements in the wild relatives of wheat are associated with recombination involving non-homoeologous chromosomes or arms during alien gene introgression under conditions that permit homoeologous recombination mediated by ph1b. Using a wheat chromosome 6A monosomic-induced 6AS*6CL Robertsonian translocation combined with ph1b-mediated recombination, we generated 17 independent recombinants carrying a new stem rust resistance gene, Sr69, from Aegilops caudata chromosome arm 6CL. Unexpectedly, 94.1% (16 of 17) of recombinants resulted from exchanges with wheat group-7 chromosomes rather than with the homoeologous group-6 chromosome. Comparative sequence- and marker-based analyses identified a 67-Mb rearranged interval on Ae. caudata 6CL that corresponds to telomeric regions of the long arms of wheat group-7 chromosomes. Sequence similarity within this interval was quantitatively associated with recombination frequency, with higher similarity corresponding to more frequent translocations. Physical and optical mapping showed that recombination within the rearranged interval generated compensating 7A/6C, 7B/6C, and 7D/6C translocations, whereas recombination outside this region produced non-compensating 6A/6C exchanges. An independent case involving the powdery mildew resistance gene Pm7C showed a similar correspondence between a rearranged 7CL region and preferential introgression into wheat 7DS. Together, these results indicate that ph1b-mediated recombination involving structurally altered chromosomes is driven by local chromosomal structure and sequence similarity rather than strict homoeologous group identity. This provides a mechanistic basis for harnessing untapped beneficial genes from structurally rearranged alien genomes. Significance StatementAlien gene introgression is a powerful strategy for wheat improvement, typically relying on ph1b-mediated recombination between homoeologous chromosomes. The genomic basis and outcomes of introgression from structurally rearranged alien chromosomes remain unclear. Here, we show that ph1b-induced recombination can efficiently target wheat-allosyntenic blocks in rearranged alien genomes, preferentially transferring genes from structurally altered alien segments into their syntenic regions on wheat chromosomes of different homoeologous groups. Crossover formation is governed by extended sequence similarity within corresponding intervals rather than strict collinearity across entire homoeologous chromosomes. As many wild species exhibit extensive genome rearrangement, these findings and methodologies expand access to underexploited genetic diversity embedded within highly rearranged wild genomes for wheat improvement.

genetics↗

bioRxiv2025

Genome assembly and population genomic analysis of Aegilops caudata uncover a rich source for disease and insect pest resistance for wheat improvement

Aegilops caudata L. is a rich source of resistance genes to major wheat pathogens and pests, yet its complex genome structure and lack of a reference sequence have hindered genetic analysis, gene discovery, and introgression. Here, we report a high-quality genome sequence assembly of Ae. caudata accession S740-69, integrated with optical mapping to precisely delineate introgressed segments from structurally altered genomic regions in wheat-Ae. caudata translocation lines carrying a novel stem rust resistance gene. Resequencing and phenotyping of 95 diverse accessions, coupled with k-mer-based association mapping, enabled population-level identification of several novel loci for resistance to wheat pests and diseases, such as greenbug and stem rust. Virus-induced gene silencing confirmed Aecau6C01G127270 (SrAect1) as the first functionally characterized stem rust resistance gene from Ae. caudata. This new genomic framework provides a foundation for systematic mining of resistance genes in this species and their efficient introgression into wheat.

genomics↗

bioRxiv2024

Opposing action of photosystem II assembly factors RBD1 and HCF136 underlies light-regulated psbA translation in plant chloroplasts

The D1 reaction center protein of photosystem II (PSII) is subject to light-induced damage. In plants, D1 photodamage activates translation of the chloroplast psbA mRNA encoding D1, providing D1 for PSII repair. Genetic data have implicated three D1 assembly factors in the regulatory mechanism: HCF244 and RBD1 activate psbA translation whereas HCF136 represses psbA translation in the dark. To clarify the regulatory circuit, we analyzed psbA ribosome occupancy in dark-adapted and illuminated rbd1 and hcf136;rbd1 double mutants in Arabidopsis, and in Zm-hcf244 and Zm-hcf136;Zm-hcf244 double mutants in maize. The results show that RBD1 is required for the light-induced recruitment of ribosomes to psbA mRNA but has little effect on psbA ribosome occupancy in the dark. Furthermore, RBD1 is dispensable for psbA translation when HCF136 is absent, indicating that RBD1 activates psbA translation indirectly, by inhibiting HCF136s repressive effect. By contrast, HCF244 is required to recruit ribosomes to psbA mRNA in light, dark, and in the absence of HCF136. These results demonstrate that the step in D1 assembly that is mediated by RBD1 is central to the perception of the D1 photodamage that triggers D1 synthesis, that RBD1 activates psbA translation in the light by relieving the repressive effect of an HCF136-dependent assembly intermediate, and that HCF244 acts independently of these events to activate psbA translation. The results implicate a feature of nascent D1 that is affected by both HCF136 and RBD1 as the signal that reports D1 photodamage to regulate psbA translation rate as needed for PSII repair. Significance StatementThe D1 subunit of photosystem II (PSII) is damaged by light and must be replaced with nascent D1 to maintain photosynthesis. In plants, D1 photodamage triggers D1 synthesis by activating translation of chloroplast psbA mRNA encoding D1. Our results demonstrate that an antagonistic interplay between two photosystem II assembly factors, HCF136 and RBD1, is at the core of the signal transduction process that senses light-induced D1 damage to regulate psbA translation. These findings implicate a feature of nascent D1 that is affected by both HCF136 and RBD1 as the signal that reports D1 photodamage to tune psbA translation as needed for PSII repair. The results elucidate an assembly-coupled translational rheostat that maintains photosynthesis in the face of PSII photodamage.

plant biology↗

bioRxiv2024

Light activates psbA translation in plants by relieving inhibition of translation factor HCF173 by the psbA ORF in cis

The D1 reaction center protein of photosystem II is subject to photooxidative damage. Photodamaged D1 must be replaced with newly synthesized D1 to maintain photosynthesis. In plant chloroplasts, D1 synthesis is coupled to D1 photodamage via regulated translation initiation on psbA mRNA, which encodes D1. Mechanisms underlying this coupling are unclear. We show by analysis of reporter constructs in tobacco that the psbA translational activators HCF173 and HCF244 activate via cis-elements in the psbA UTRs and that the 5 UTR sequence bound by HCF173 is essential for psbA expression. However, the psbA UTRs are not sufficient to program light-regulated translation. Instead, the psbA open reading frame acts in cis to repress translation initiation, and D1 photodamage relieves this repression. A truncated HCF173 mutant conditions constitutively high psbA ribosome occupancy in the dark, implicating HCF173 as a mediator of the repressive signal. We propose a model that is informed by structures of the Complex I assembly factor CIA30/NDUFAF1 positing that D1 photodamage relieves a repressive cotranslational interaction between nascent D1 and HCF173s CIA30 domain, and that the D1 assembly factor HCF136 promotes this interaction. These findings elucidate a translational rheostat that maintains photosynthesis in the face of inevitable photosystem II photodamage.

plant biology↗

bioRxiv2024

Localization of Proteins Involved in the Biogenesis of the Photosynthetic Apparatus to Thylakoid Subdomains in Arabidopsis

Thylakoid membranes in chloroplasts and cyanobacteria harbor the multisubunit protein complexes that catalyze the light reactions of photosynthesis. In plant chloroplasts, the thylakoid membrane system comprises a highly organized network with several subcompartments that differ in composition and morphology: grana stacks, unstacked stromal lamellae, and grana margins at the interface between stacked and unstacked regions. The localization of components of the photosynthetic apparatus among these subcompartments has been well characterized. However, less is known about the localization of proteins involved in the biogenesis and repair of the photosynthetic apparatus, the partitioning of proteins between two recently resolved components of the traditional margin fraction (refined margins and curvature), and the effects of light on these features. In this study, we analyzed the partitioning of numerous thylakoid biogenesis and repair factors among grana, curvature, refined margin, and stromal lamellae fractions of Arabidopsis thylakoid membranes, comparing the results from illuminated and dark-adapted plants. Several proteins previously shown to localize to a margin fraction partitioned in varying ways among the resolved curvature and refined margin fractions. For example, the ALB3 insertase and FtsH protease involved in photosystem II (PSII) repair were concentrated in the refined margin fraction, whereas TAT translocon subunits and proteins involved in early steps in photosystem assembly were concentrated in the curvature fraction. By contrast, two photosystem assembly factors that facilitate late assembly steps were depleted from the curvature fraction. The enrichment of the PSII subunit OE23/PsbP in the curvature fraction set it apart from other PSII subunits, supporting the previous conjecture that OE23/PsbP assists in PSII biogenesis and/or repair. The PSII assembly factor PAM68 partitioned differently among thylakoid fractions from dark-adapted plants and illuminated plants, and was the only analyzed protein to convincingly do so. These results demonstrate an unanticipated spatial heterogeneity of photosystem biogenesis and repair functions in thylakoid membranes, and reveal the curvature fraction to be a focal point of early photosystem biogenesis.

plant biology↗

bioRxiv2024

Translational activation by a synthetic PPR protein elucidates control of psbA translation in Arabidopsis chloroplasts

Translation initiation on psbA mRNA in plant chloroplasts scales with light intensity, providing its gene product, D1, to replace photodamaged D1 in Photosystem II. The psbA translational activator HCF173 has been hypothesized to mediate this regulation. HCF173 belongs to the short-chain dehydrogenase/reductase superfamily, associates with the psbA 5-untranslated region (5-UTR), and has been hypothesized to enhance translation by binding an RNA segment that would otherwise pair with and mask the ribosome binding region. To test these hypotheses, we examined whether a synthetic pentatricopeptide repeat (sPPR) protein can substitute for HCF173 when bound to the HCF173 binding site. We show that an sPPR designed to bind HCF173s footprint in the psbA 5-UTR bound the intended site in vivo and partially substituted for HCF173 to activate psbA translation. However, sPPR-activated translation did not respond to light. These results imply that HCF173 activates translation, at least in part, by sequestering the RNA it binds to maintain an accessible ribosome binding region, and that HCF173 is also required to regulate psbA translation in response to light. Translational activation can be added to the functions that can be programmed with sPPR proteins for synthetic biology applications in chloroplasts. One sentence summaryA synthetic PPR protein substitutes for HCF173, a non-PPR translational activator in chloroplasts, elucidating HCF173 functions and demonstrating the ability of synthetic PPRs to activate translation.

plant biology↗

bioRxiv2022

Correlated retrograde and developmental regulons implicate multiple retrograde signals as coordinators of chloroplast development in maize

Signals emanating from chloroplasts influence nuclear gene expression, but roles of retrograde signals during chloroplast development are unclear. To address this gap, we analyzed transcriptomes of four non-photosynthetic maize mutants and interpreted them in the context of transcriptome dynamics during normal leaf development. We analyzed two albino mutants lacking plastid ribosomes and two chlorotic mutants with thylakoid targeting or plastid transcription defects. The [~]2700 differentially expressed genes fall into six major categories based on the polarity and mutant-specificity of the change. These distinct retrograde responses correlate with distinct developmental dynamics, with down-regulated genes expressed later in normal development and up-regulated genes acting early. Photosynthesis genes are down-regulated specifically in the albino mutants, whereas up-regulated genes are enriched for functions in chloroplast biogenesis and cytosolic translation. TOR signaling is elevated in plastid ribosome-deficient mutants and declines in concert with plastid ribosome buildup during leaf development. Our results implicate three plastid signals as integral players during photosynthetic differentiation. One signal requires plastid ribosomes and activates photosynthesis genes. A second signal reflects attainment of chloroplast maturity and represses chloroplast biogenesis genes. A third signal responds to nutrient consumption by developing chloroplasts and represses TOR, which down-regulates cell proliferation genes early in leaf development. One sentence summaryTranscriptomes of non-photosynthetic maize mutants when interpreted in the context of normal developmental dynamics implicate three plastid signals as coordinators of photosynthetic differentiation. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (https://academic.oup.com/plcell/pages/General-Instructions) is Alice Barkan (abarkan@uoregon.edu)

plant biology↗

bioRxiv2020

Ribosome profiling elucidates the contribution of differential translation to differential gene expression in bundle sheath and mesophyll cells in maize

The efficiencies offered by C4 photosynthesis have motivated efforts to understand its biochemical, genetic and developmental basis. Reactions underlying C4 traits in most C4 plants are partitioned between two cell types, bundle sheath (BS) and mesophyll (M) cells. RNA-seq has been used to catalog differential gene expression in BS and M cells in maize and several other C4 species. However, the contribution of translational control to maintaining the distinct proteomes of BS and M cells has not been addressed. In this study, we used ribosome profiling (ribo-seq) and RNA-seq to describe translatomes, translational efficiencies, and microRNA abundance in BS and M-enriched fractions of maize seedling leaves. A conservative interpretation of our data revealed 182 genes exhibiting cell-type dependent differences in translational efficiency, 31 of which encode proteins with core roles in C4 photosynthesis. Our results suggest that non-AUG start codons are used preferentially in upstream open reading frames of BS cells, revealed mRNA sequence motifs that correlate with cell type-dependent translation, and identified potential translational regulators that are differentially expressed. In addition, our data expand the set of genes known to be differentially expressed in BS and M cells, including genes encoding transcription factors and microRNAs. These data add to the resources for understanding the evolutionary and developmental basis of C4 photosynthesis and for its engineering into C3 crops.

plant biology↗

bioRxiv2020

Light-induced psbA translation in plants is triggered by photosystem II damage via an assembly-linked autoregulatory circuit

The D1 reaction center protein of Photosystem II (PSII) is subject to light-induced damage. Degradation of damaged D1 and its replacement by nascent D1 are at the heart of a PSII repair cycle, without which photosynthesis is inhibited. In mature plant chloroplasts, light stimulates the recruitment of ribosomes specifically to psbA mRNA to provide nascent D1 for PSII repair, and also triggers a global increase in translation elongation rate. The light-induced signals that initiate these responses are unclear. We present action spectrum and genetic data indicating that the light-induced recruitment of ribosomes to psbA mRNA is triggered by D1 photodamage, whereas the global stimulation of translation elongation is triggered by photosynthetic electron transport. Furthermore, mutants lacking HCF136, which mediates an early step in D1 assembly, exhibit constitutively high psbA ribosome occupancy in the dark, and differ in this way from mutants lacking PSII for other reasons. These results, together with the recent elucidation of a thylakoid membrane complex that functions in PSII assembly, PSII repair and psbA translation, suggest an autoregulatory mechanism in which the light-induced degradation of D1 relieves repressive interactions between D1 and translational activators in the complex. We suggest that the presence of D1 in this complex coordinates D1 synthesis with the need for nascent D1 during both PSII biogenesis and PSII repair in plant chloroplasts. Significance StatementPhotosystem II (PSII) harbors the water-splitting activity underlying oxygenic photosynthesis. The PSII reaction center protein D1 is subject to photodamage and must be replaced with nascent D1 to maintain photosynthetic activity. How new D1 synthesis is coordinated with D1 damage has been a long-standing question. Our results clarify the nature of the light-induced signal that activates D1 synthesis for PSII repair in plants, and suggest an autoregulatory mechanism in which degradation of damaged D1 relieves a repressive interaction between D1 and translational activators in a complex that functions in PSII assembly and repair. This proposed mechanism comprises a responsive switch that couples D1 synthesis to need for D1 during PSII biogenesis and repair.

plant biology↗