Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region.

Equisetum is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. Equisetum is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails (Equisetum, Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in Equisetum remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of Equisetum, and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of Equisetum. The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of Equisetum plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes accD and ycf1 can be used as potential DNA barcodes for the identification and phylogeny of the genus Equisetum. Twelve photosynthesis-related genes were specifically selected in Equisetum. Comparative genomic analyses implied divergent evolutionary patterns between Equisetum and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between Equisetum and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between Equisetum species, and also provide genomic resources for the study of Equisetum systematics and evolution.

RABL2 promotes the outward transition zone passage of signaling proteins in cilia via ARL3.

Certain transmembrane and membrane-tethered signaling proteins export from cilia as BBSome cargoes via the outward BBSome transition zone (TZ) diffusion pathway, indispensable for maintaining their ciliary dynamics to enable cells to sense and transduce extracellular stimuli inside the cell. Murine Rab-like 2 (Rabl2) GTPase resembles Chlamydomonas Arf-like 3 (ARL3) GTPase in promoting outward TZ passage of the signaling protein cargo-laden BBSome. During this process, ARL3 binds to and recruits the retrograde IFT train-dissociated BBSome as its effector to diffuse through the TZ for ciliary retrieval, while how RABL2 and ARL3 cross talk in this event remains uncertain. Here, we report that Chlamydomonas RABL2 in a GTP-bound form (RABL2GTP) cycles through cilia via IFT as an IFT-B1 cargo, dissociates from retrograde IFT trains at a ciliary region right above the TZ, and converts to RABL2GDP for activating ARL3GDP as an ARL3 guanine nucleotide exchange factor. This confers ARL3GTP to detach from the ciliary membrane and become available for binding and recruiting the phospholipase D (PLD)-laden BBSome, autonomous of retrograde IFT association, to diffuse through the TZ for ciliary retrieval. Afterward, RABL2GDP exits cilia by being bound to the ARL3GTP/BBSome entity as a BBSome cargo. Our data identify ciliary signaling proteins exported from cilia via the RABL2-ARL3 cascade-mediated outward BBSome TZ diffusion pathway. According to this model, hedgehog signaling defect-induced Bardet-Biedl syndrome caused by RABL2 mutations in humans could be well explained in a mutation-specific manner, providing us with a mechanistic understanding behind the outward BBSome TZ passage required for proper ciliary signaling.

Simplified Genomic Data Revealing the Decline of Aleuritopteris grevilleoides Population Accompanied by the Uplift of Dry-Hot Valley in Yunnan, China.

Understanding the evolutionary history of endangered species is crucial for identifying the main reasons for species endangerment in the past and predicting the changing trends and evolutionary directions of their future distribution. In order to study the impact of environmental changes caused by deep valley incision after the uplift of the Qinghai-Tibet Plateau on endangered species, we collected 23 samples belonging to four populations of Aleuritopteris grevilleoides, an endangered fern endemic to the dry-hot valleys (DHV) of Yunnan. Single-nucleotide variation sites (SNPs) were obtained by the genotyping-by-sequencing (GBS) method, and approximately 8085 SNP loci were identified. Through the reconstruction and analysis of genetic diversity, population structure, population dynamics, evolution time, and ancestral geographical distribution, combined with geological historical events such as the formation of dry-hot valleys, this study explores the formation history, current situation, reasons for endangerment and scientifically sound measures for the protection of A. grevilleoides. In our study, A. grevilleoides had low genetic diversity (Obs_Het = 0.16, Exp_Het = 0.32, Pi = 0.33) and a high inbreeding coefficient (Fis = 0.45). The differentiation events were 0.18 Mya, 0.16 Mya, and 0.11 Mya in the A. grevilleoides and may have been related to the formation of terraces within the dry-hot valleys. The history of population dynamics results shows that the diversion of the river resulted in a small amount of gene flow between the two clades, accompanied by a rapid increase in the population at 0.8 Mya. After that, the effective population sizes of A. grevilleoides began to contract continuously due to topographic changes resulting from the continuous expansion of dry-hot valleys. In conclusion, we found that the environmental changes caused by geological events might be the main reason for the changing population size of A. grevilleoides.

Functional characterization of GATA6 genetic variants associated with mild congenital heart defects.

Damaging GATA6 variants can cause moderate congenital heart defects. With the application of next-generation sequencing approaches, various novel GATA6 variants with unknown significance have been identified from a broad spectrum of congenital heart defects. However, functional assessment for distinct GATA6 variants from different severity of congenital heart defects, especially from mild defects, is lacking, which hinders our understanding of the genotype-phenotype correlations and underlying mechanisms. Here, we assessed the functional consequences of nine rare GATA6 variants, which had been implicated as the most significant variants associated with mild congenital heart defects using the largest case and control cohort. We examined the effects of these variants on subcellular localization, transcriptional activity, and protein interactions in 293T or AC16 cells and their ability to rescue heart malformation in gata6 zebrafish mutant. We found that two of these nine variants, Q120X and S424I, significantly decreased transcriptional activity. Additionally, Q120X altered subcellular localization. Consistent with the in vitro results, the in vivo results showed that Q120X and S424I lost their potency to rescue ventricular malformation in gata6 -/- embryos. The results indicated that Q120X and S424I are pathogenic in mild congenital heart defects. Further, the inconsistence of severely impaired Q120X function and mild CHDs phenotype suggested the complexity of the genotype-phenotype correlation between the GATA6 variant and heart phenotype, which may help to inform prenatal genetic counseling and pre-implantation genotyping for congenital heart defects.

ARL3 mediates BBSome ciliary turnover by promoting its outward movement across the transition zone.

Ciliary receptors and their certain downstream signaling components undergo intraflagellar transport (IFT) as BBSome cargoes to maintain their ciliary dynamics for sensing and transducing extracellular stimuli inside the cell. Cargo-laden BBSomes pass the transition zone (TZ) for ciliary retrieval, but how this passage is controlled remains elusive. Here, we show that phospholipase D (PLD)-laden BBSomes shed from retrograde IFT trains at the proximal ciliary region right above the TZ to act as Arf-like 3 (ARL3) GTPase-specific effectors in Chlamydomonas cilia. Under physiological condition, ARL3GDP binds to the membrane for diffusing into cilia. Following nucleotide exchange, ARL3GTP detaches from the ciliary membrane, binds to retrograde IFT train-shed and PLD-laden BBSomes at the proximal ciliary region right above the TZ, and recruits them to pass the TZ for ciliary retrieval likely via diffusion. ARL3 mediates the ciliary dynamics of certain signaling molecules through facilitating BBSome ciliary retrieval, providing a mechanistic understanding behind why ARL3-related Joubert syndrome shares overlapping phenotypes with Bardet-Biedl syndrome.

The Significance of Symptoms in Predicting Coronary Artery Aneurysms of Kawasaki Disease, Especially in Female Patients.

Background: Kawasaki disease (KD) is an acute febrile systemic vasculitis of unknown etiology that occurs during early childhood, commonly involving the coronary artery, and can lead to coronary artery aneurysms (CAAs). Methods: The demographic, clinical, and laboratory data of KD patients without coronary artery lesions (N-CAL) and with CAA were collected during 2005-2020 at the Second Affiliated Hospital of Wenzhou Medical University. The patients were divided into the development cohort and the validation cohort. First, we compared the general information, symptoms, and laboratory data of N-CAL and CAA patients in the development cohort and the total cohort and screened out the different indices by logistic regression analysis. Then, we established three models and compared the area under the curve (AUC) values of the receiver operating characteristic (ROC) curves to identify meaningful models for CAA, which were further verified by decision curve analysis (DCA). Second, taking into account previous reports on the importance of gender to CAA, gender stratification was conducted. Results: The analysis of clinical and blood indices revealed the following novel features: (i) Many factors were found to be related to CAA, including IVIG resistance and the symptoms of rash, oral changes, and cervical lymphadenopathy. (ii) The development cohort was analyzed by logistic regression, and three models were established. The ROC curves showed that Model 2, composed of IVIG resistance, rash, oral changes, and cervical lymphadenopathy, had a better AUC value and easily to evaluate in the prediction of CAA. (iii) The selected model for predicting CAA in the development cohort was further confirmed in the validation cohort through DCAs. (iv)We further compared the items enrolled in the three models above between the N-CAL and CAA groups by sex, and the results indicated that female KD patients without rash, oral changes, and cervical lymphadenopathy were more likely to develop CAA. Conclusion: The absence of rash, oral changes, and cervical lymphadenopathy are risk factors for CAA, especially in female KD patients. Accurately recognizing symptoms, early diagnosis, and standard treatment for KD are key to reducing the incidence of CAA.

Overexpression of histone demethylase gene SlJMJ524 from tomato confers Cd tolerance by regulating metal transport-related protein genes and flavonoid content in Arabidopsis.

Cadmium (Cd), as a heavy metal, not only negatively affects the development and yield of plants, but also threatens human health due to its accumulation in plants. Increasing evidences indicate that the JUMONJI-C DOMAIN-CONTAINING PROTEIN (JMJ) gene family plays a key role in regulating plant development and stress. Therefore, in this study, SlJMJ524, a 1254 bp gene encoding the jumonji C domain (417 amino acids), was highly expressed in tomato leaves and flowers. Interestingly, the transgenic plants exhibited sensitivity to Cd during post-germination stage but showed enhanced tolerance to the heavy metal during adult stage. Overexpression of SlJMJ524 increased the expression level of related proteins gene involved in heavy metal uptake while increasing Cd tolerance through the GSH-PC pathway. The higher transcription of genes related to flavonoid synthesis reflected higher accumulations of flavonoids in transgenic plants. Our study demonstrated that the ectopic expression of SlJMJ524 conferred the transgenic plants many traits for improving cadmium stress tolerance at different developmental stages. This study advances our collective understanding of the functional role of JMJs and can be used to improve the cadmium tolerance and breeding of crops and plants.

Chlamydomonas LZTFL1 mediates phototaxis via controlling BBSome recruitment to the basal body and its reassembly at the ciliary tip.

Many G protein-coupled receptors and other signaling proteins localize to the ciliary membrane for regulating diverse cellular processes. The BBSome composed of multiple Bardet-Biedl syndrome (BBS) proteins is an intraflagellar transport (IFT) cargo adaptor essential for sorting signaling proteins in and/or out of cilia via IFT. Leucine zipper transcription factor-like 1 (LZTFL1) protein mediates ciliary signaling by controlling BBSome ciliary content, reflecting how LZTFL1 mutations could cause BBS. However, the mechanistic mechanism underlying this process remains elusive thus far. Here, we show that LZTFL1 maintains BBSome ciliary dynamics by finely controlling BBSome recruitment to the basal body and its reassembly at the ciliary tip simultaneously in Chlamydomonas reinhardtii LZTFL1 directs BBSome recruitment to the basal body via promoting basal body targeting of Arf-like 6 GTPase BBS3, thus deciding the BBSome amount available for loading onto anterograde IFT trains for entering cilia. Meanwhile, LZTFL1 stabilizes the IFT25/27 component of the IFT-B1 subcomplex in the cell body so as to control its presence and amount at the basal body for entering cilia. Since IFT25/27 promotes BBSome reassembly at the ciliary tip for loading onto retrograde IFT trains, LZTFL1 thus also directs BBSome removal out of cilia. Therefore, LZTFL1 dysfunction deprives the BBSome of ciliary presence and generates Chlamydomonas cells defective in phototaxis. In summary, our data propose that LZTFL1 maintains BBSome dynamics in cilia by such a dual-mode system, providing insights into how LZTFL1 mediates ciliary signaling through maintaining BBSome ciliary dynamics and the pathogenetic mechanism of the BBS disorder as well.

Bardet-Biedl syndrome 3 protein promotes ciliary exit of the signaling protein phospholipase D via the BBSome.

Certain ciliary signaling proteins couple with the BBSome, a conserved complex of Bardet-Biedl syndrome (BBS) proteins, to load onto retrograde intraflagellar transport (IFT) trains for their removal out of cilia in Chlamydomonas reinhardtii. Here, we show that loss of the Arf-like 6 (ARL6) GTPase BBS3 causes the signaling protein phospholipase D (PLD) to accumulate in cilia. Upon targeting to the basal body, BBSomes enter and cycle through cilia via IFT, while BBS3 in a GTP-bound state separates from BBSomes, associates with the membrane, and translocates from the basal body to cilia by diffusion. Upon arriving at the ciliary tip, GTP-bound BBS3 binds and recruits BBSomes to the ciliary membrane for interacting with PLD, thus making the PLD-laden BBSomes available to load onto retrograde IFT trains for ciliary exit. Therefore, BBS3 promotes PLD exit from cilia via the BBSome, providing a regulatory mechanism for ciliary signaling protein removal out of cilia.

Analysis of 2,4-epibrassinolide created an enhancement tolerance on Cd toxicity in Solanum nigrum L.

Contamination of soils with cadmium (Cd) is a serious problem worldwide. Solanum nigrum L. is reported as a Cd hyperaccumulator, but its enrichment capacity is limited. 2,4-Epibrassinolide (2,4-EBL) plays important roles in plant response to various stresses. Little is known about its effect on Cd tolerance in S. nigrum. Current study was performed to demonstrate effects of 2,4-EBL on plant growth, photosynthesis activity, activities of antioxidants, and Cd concentration in plants by nutrient solution contaminated with Cd. Results revealed that S. nigrum exhibited toxicity to Cd stress, including reducing plant height, root length, and chlorophyll content and increasing malondialdehyde (MDA) content. Exogenous application of 2,4-EBL significantly enhanced the contents of proline and soluble sugar and decreased the MDA content. Meanwhile, the levels of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) markedly increased compared with the control. Interesting, 2,4-EBL promoted photosynthesis by increasing the chlorophyll content, Fv/Fm. And increase in chlorophyll content is caused by increased expression of synthetic genes and decreased expression of degraded genes. 2,4-EBL also decreased accumulation of Cd in S. nigrum compared with single Cd stress. According to the present results, 2,4-EBL can effectively be used to alleviate the damage of Cd stress in S. nigrum and probably in other solanaceae.

Modification of cardiac transcription factor Gata6 by SUMO.

SUMOylation, covalent conjugation of small ubiquitin-related modifier (SUMO), has been emerging as a critical posttranslational modification of developmental transcription factors, as well as key regulators in the adult heart. Identifying the SUMOylated targets within cardiac transcription factors will facilitate to unravel the roles of SUMOylation in heart development and disease. Here, we show that Gata6, an essential cardiac transcription factor, can be modified by SUMO in vivo. Mutation of potential SUMOylation sites reveals that a lysine residue at amino acid position 12 of Gata6 serves as the major attachment site for SUMO. Pias1, as an E3 SUMO ligase, preferentially enhances the conjugation of SUMO1 to Gata6 through its RING finger domain. Functional analyses with SUMOylation-deficient mutant indicate that SUMOylation does not affect the subcellular localization but instead represses Gata6 transcriptional activity. Our data suggest that posttranslational modification of Gata6 by SUMO conjugation provides a novel mechanism to regulate Gata6 activity.

Climate Is Not All: Evidence From Phylogeography of Rhodiola fastigiata (Crassulaceae) and Comparison to Its Closest Relatives.

How geological events and climate oscillations in the Pleistocene glaciation shaped the geographic distribution of genetic variation of species on the Qinghai-Tibetan Plateau (QTP) and its adjacent areas has been extensively studied. However, little studies have investigated whether closely related species in the same genus with similar physiological and life history traits responded similarly to the glacial climatic oscillations. If this is not the case, we would expect that the population histories of studied species were not driven by extrinsic environmental changes alone. Here we conducted a phylogeographic study of a succulent alpine plant Rhodiola fastigiata, using sequences from chloroplast genome and nrITS region, as well as ecological niche modeling. The results of R. fastigiata were compared to other congeneric species that have been studied, especially to R. alsia and R. crenulata. We found that for both markers, two geographic groups could be revealed, corresponding to the QTP plateau and the Hengduan Mountains, respectively, indicating isolated refugia in those two areas. The two groups diverged 1.23 Mya during the Pleistocene. We detected no significant population expansion by mismatch distribution analysis and Bayesian Skyline Plot. We found that even these similar species with similar physiological and life history traits have had different demographic histories in the Quaternary glacial periods. Our comparative phylogeographic study sheds new lights into phylogeographic research that extrinsic environmental changes are not the only factor that can drive population demography, and other factors, such as coevolved interactions between plants and their specialized pathogens, that probably played a role need to be examined with more case studies.