In Arabidopsis thaliana, each ribosomal protein (RP) is encoded by a small gene family consisting of two or more highly homologous paralogues, which results in ribosome heterogeneity. It is largely unknown that how genes from multiple member containing RP families are regulated at transcriptional level to accommodate the needs of different plant organs and developmental stages. In this study, we investigated the transcript accumulation profiles of RP genes and found that the expression levels of RP genes are varied dramatically in different organs and developmental stages. Although most RP genes are found to be ubiquitously transcribed, some are obviously transcribed with spatiotemporal specificity. The hierarchical clustering trees of transcript accumulation intensity of RP genes revealed that different organs and developmental stages have different population of RP gene transcripts. By interrogating of the expression fluctuation trend of RP genes, we found that in spite of the fact that most groups of paralogous RP genes are transcribed in concerted manners, some RPs gene have contrasting expression patterns. When transcripts of paralogous RP genes from the same family are considered together, the expression level of most RP genes are well-matched but some are obviously higher or lower, therefore we speculate that some superfluous RPs may act outside the ribosome and a portion of ribosomes may lack one or even more RP(s). Altogether, our analysis results suggested that functional divergence may exist among heterogeneous ribosomes that resulted from different combination of RP paralogues, and substoichiometry of several RP gene families may lead to another layer of heterogeneous ribosomes which also have divergent functions in plants.

Background

In plants, each ribosomal protein (RP) is encoded by a small gene family but it is largely unknown whether the family members are functionally diversified. There are two RPL23a paralogous genes (RPL23aA and RPL23aB) encoding cytoplasmic ribosomal proteins in Arabidopsis thaliana. Knock-down of RPL23aA using RNAi impeded growth and led to morphological abnormalities, whereas knock-out of RPL23aB had no observable phenotype, thus these two RPL23a paralogous proteins have been used as examples of ribosomal protein paralogues with functional divergence in many published papers.

Results

In this study, we characterized T-DNA insertion mutants of RPL23aA and RPL23aB. A rare non-allelic non-complementation phenomenon was found in the F1 progeny of the rpl23aa X rpl23ab cross, which revealed a dosage effect of these two genes. Both RPL23aA and RPL23aB were found to be expressed almost in all examined tissues as revealed by GUS reporter analysis. Expression of RPL23aB driven by the RPL23aA promoter can rescue the phenotype of rpl23aa, indicating these two proteins are actually equivalent in function. Interestingly, based on the publicly available RNA-seq data, we found that these two RPL23a paralogues were expressed in a concerted manner and the expression level of RPL23aA was much higher than that of RPL23aB at different developmental stages and in different tissues.

Conclusions

Our findings suggest that the two RPL23a paralogous proteins are functionally equivalent but the two genes are not. RPL23aA plays a predominant role due to its higher expression levels. RPL23aB plays a lesser role due to its lower expression. The presence of paralogous genes for the RPL23a protein in plants might be necessary to maintain its adequate dosage.

Plant TRANS-ACTING SIRNA3 (TAS3)-derived short interfering RNAs (siRNAs) include tasiR-AUXIN RESPONSE FACTORs (ARFs), which are functionally conserved in targeting ARF genes, and a set of non-tasiR-ARF siRNAs, which have rarely been studied. In this study, TAS3 siRNAs were systematically characterized in rice (Oryza sativa). Small RNA sequencing results showed that an overwhelming majority of TAS3 siRNAs belong to the non-tasiR-ARF group, while tasiR-ARFs occupy a diminutive fraction. Phylogenetic analysis of TAS3 genes across dicot and monocot plants revealed that the siRNA-generating regions were highly conserved in grass species, especially in the Oryzoideae. Target genes were identified for not only tasiR-ARFs but also non-tasiR-ARF siRNAs by analyzing rice Parallel Analysis of RNA Ends datasets, and some of these siRNA-target interactions were experimentally confirmed using tas3 mutants generated by genome editing. Consistent with the de-repression of target genes, phenotypic alterations were observed for mutants in three TAS3 loci in comparison to wild-type rice. The regulatory role of ribosomes in the TAS3 siRNA-target interactions was further revealed by the fact that TAS3 siRNA-mediated target cleavage, in particular tasiR-ARFs targeting ARF2/3/14/15, occurred extensively in rice polysome samples. Altogether, our study sheds light into TAS3 genes in plants and expands our knowledge about rice TAS3 siRNA-target interactions.

MicroRNAs (miRNAs) play crucial roles in gene expression regulation through RNA cleavage or translation repression. Here, we report the identification of an evolutionarily conserved WD40 domain protein as a player in miRNA biogenesis in Arabidopsis thaliana. A mutation in the REDUCTION IN BLEACHED VEIN AREA (RBV) gene encoding a WD40 domain protein led to the suppression of leaf bleaching caused by an artificial miRNA; the mutation also led to a global reduction in the accumulation of endogenous miRNAs. The nuclear protein RBV promotes the transcription of MIR genes into pri-miRNAs by enhancing the occupancy of RNA polymerase II (Pol II) at MIR gene promoters. RBV also promotes the loading of miRNAs into AGO1. In addition, RNA-seq revealed a global splicing defect in the mutant. Thus, this evolutionarily conserved, nuclear WD40 domain protein acts in miRNA biogenesis and RNA splicing.

MicroRNA156 (miR156) and miR529 have high sequence similarity and recognize overlapping sites in the same target genes, SQUAMOSA promoter binding protein-like (SPL or SBP box) genes, making it difficult to accurately distinguish their roles in regulatory networks that affect numerous biological functions. Here, we collected data about miR156 and miR529 family members from representative land plants and performed sequence comparisons, phylogenetic analysis, small RNA sequencing, and parallel analysis of RNA ends (PARE) analysis to dissect their evolutionary and functional differences. Although miR156 and miR529 are highly similar, there are differences in their mismatch-sensitive regions, which are essential for target recognition. In land plants, miR156 precursors are conserved mainly within the hairpin region, whereas miR529 precursors are conserved outside the hairpin region, including both the 5' and 3' arms. Phylogenetic analysis showed that MIR156 and MIR529 evolved independently, through divergent evolutionary patterns. The two genes also exhibit different expression patterns, with MIR529 preferentially expressed in reproductive tissues and MIR156 in other tissues. PARE analysis revealed that miR156 and miR529 possess specific targets in addition to common targets in maize, pointing to functional differences between them. Based on our findings, we developed a method for the rapid identification of miR529 and miR156 family members and uncovered the evolutionary divergence of these families, providing insights into their different regulatory roles in plant growth and development.

In tomato, SlNOR and SlNOR-like1, members of the NAC family of transcription factors (TFs), are known to play critical roles in regulating fruit ripening and are highly expressed in floral organs. However, their role in flower development remains unclear. In this study, we generated and functionally characterized a double knockout mutant, nor/nor-like1. Our findings reveal that the pollen abortion of the nor/nor-like1 impedes ovarian enlargement, resulting in fruit formation failure. Histological analyses demonstrate that the pollen wall collapse occurs during the mature pollen stage and leads to the abnormal pollen wall component deposition at the microspore stage, resulting in the male sterility in the double knockout mutant lines. Kyoto Encyclopedia of Genes and Genomes enrichment pathway analyses further suggest that the loss of SlNOR and SlNOR-like1 function affects several metabolic pathways related to pollen development, including ABC transporters, lipid metabolism, phenylpropanoid biosynthesis, hormone signal transduction, starch and sucrose metabolism, and cutin, suberine, and wax biosynthesis. Furthermore, our results demonstrate that SlNOR and SlNOR-like1 could directly bind to the promoters of key genes associated with pollen wall formation and activate their expression, including ATP-binding cassette transporters of the G family (SlABCG8/9/23), ECERIFERUM (SlCER1), and glycine-rich protein (SlGRP92). These findings suggest that SlNOR and SlNOR-like1 may play a redundant role in the biosynthesis and transport of sporopollenin precursors, cuticular wax biosynthesis, and exine formation. In summary, our study highlights a previously uncharacterized role of SlNOR and SlNOR-like1 in tomato pollen wall formation and male fertility.

We explore the influence of radio-mode feedback on the properties of the cool circumgalactic medium (CGM). To this end, we assemble a statistical sample of approximately 30,000 radio galaxies with background quasars by combining optical spectroscopic measurements of luminous red galaxies and quasars from the year 1 data set of the Dark Energy Spectroscopic Instrument and radio sources from the LOw-Frequency ARray Two-metre Sky Survey (LoTSS) DR2 catalog and the Very Large Array Sky Survey (VLASS) quick-look catalog. Galaxies with similar optical properties but with no radio counterparts in LoTSS and VLASS are selected as the control group. We measure the cool CGM properties of radio galaxies and their control samples traced by Mg ii absorption lines, including covering fraction, rest equivalent width, and gas kinematics. Our results show no significant difference in the properties of gas around radio galaxies and their control sample, indicating that the operating radio-mode feedback of massive galaxies does not produce detectable effects on the properties of the cool CGM. Finally, we show that the CGM of radio galaxies contains a nonnegligible amount of cool gas with approximately 1010 M ⊙. This abundance can place a stringent constraint on the radio-mode feedback models.

We present findings of the detection of Magnesium II (Mg ii, λ = 2796, 2803 Å) absorbers from the early data release of the Dark Energy Spectroscopic Instrument (DESI). DESI is projected to obtain spectroscopy of approximately 3 million quasars (QSOs), of which over 99% are anticipated to be at redshifts greater than z > 0.3, such that DESI would be able to observe an associated or intervening Mg ii absorber illuminated by the background QSO. We have developed an autonomous supplementary spectral pipeline that detects these systems through an initial line-fitting process and then confirms the line properties using a Markov Chain Monte Carlo sampler. Based upon a visual inspection of the resulting systems, we estimate that this sample has a purity greater than 99%. We have also investigated the completeness of our sample in regard to both the signal-to-noise properties of the input spectra and the rest-frame equivalent width (W 0) of the absorber systems. From a parent catalog containing 83,207 quasars, we detect a total of 23,921 Mg ii absorption systems following a series of quality cuts. Extrapolating from this occurrence rate of 28.8% implies a catalog at the completion of the five-year DESI survey that will contain over eight hundred thousand Mg ii absorbers. The cataloging of these systems will enable significant further research because they carry information regarding circumgalactic medium environments, the distribution of intervening galaxies, and the growth of metallicity across the redshift range 0.3 ≤ z < 2.5.

We study the [O ii] profiles of emission-line galaxies (ELGs) from the Early Data Release of the Dark Energy Spectroscopic Instrument (DESI). To this end, we decompose and classify the shape of [O ii] profiles with the first two eigenspectra derived from principal component analysis. Our results show that DESI ELGs have diverse line profiles, which can be categorized into three main types: (1) narrow lines with a median width of ∼50 km s−1, (2) broad lines with a median width of ∼80 km s−1, and (3) two redshift systems with a median velocity separation of ∼150 km s−1, i.e., double-peak galaxies. To investigate the connections between the line profiles and galaxy properties, we utilize the information from the COSMOS data set and compare the properties of ELGs, including star formation rate (SFR) and galaxy morphology, with the average properties of reference star-forming galaxies with similar stellar mass, sizes, and redshifts. Our findings show that, on average, DESI ELGs have a higher SFR and more asymmetrical/disturbed morphology than the reference galaxies. Moreover, we uncover a relationship between the line profiles, the excess SFR, and the excess asymmetry parameter, showing that DESI ELGs with broader [O ii] line profiles have more disturbed morphology and higher SFR than the reference star-forming galaxies. Finally, we discuss possible physical mechanisms giving rise to the observed relationship and the implications of our findings on the galaxy clustering measurements, including the halo occupation distribution modeling of DESI ELGs and the observed excess velocity dispersion of the satellite ELGs.

The Dark Energy Spectroscopic Instrument (DESI) is carrying out a five-year survey that aims to measure the redshifts of tens of millions of galaxies and quasars, including 8 million luminous red galaxies (LRGs) in the redshift range 0.4 < z ≲ 1.0. Here we present the selection of the DESI LRG sample and assess its spectroscopic performance using data from Survey Validation (SV) and the first two months of the Main Survey. The DESI LRG sample, selected using g, r, z, and W1 photometry from the DESI Legacy Imaging Surveys, is highly robust against imaging systematics. The sample has a target density of 605 deg−2 and a comoving number density of 5 × 10−4 h3 Mpc−3 in 0.4 < z < 0.8; this is a significantly higher density than previous LRG surveys (such as SDSS, BOSS, and eBOSS) while also extending to z ∼ 1. After applying a bright star veto mask developed for the sample, 98.9% of the observed LRG targets yield confident redshifts (with a catastrophic failure rate of 0.2% in the confident redshifts), and only 0.5% of the LRG targets are stellar contamination. The LRG redshift efficiency varies with source brightness and effective exposure time, and we present a simple model that accurately characterizes this dependence. In the appendices, we describe the extended LRG samples observed during SV.