Biology subjects

Vijayraghavan, U.

Publications and source records attributed to Vijayraghavan, U..

4 recordsLinked to original sources

bioRxiv2024

Prp16 enables efficient splicing of introns with diverse exonic consensus elements in the short-intron rich Cryptococcus neoformans transcriptome

The DEAH box splicing helicase Prp16 in budding yeast governs spliceosomal remodeling from the branching conformation (C complex) to the exon ligation conformation (C* complex). In this study, we examined the genome-wide functions of Prp16 in the short intron-rich genome of the basidiomycete yeast Cryptococcus neoformans. The presence of multiple introns per transcript with intronic features more similar to higher eukaryotes makes it a promising model to study spliceosomal splicing. Using a promoter-shutdown conditional Prp16 knockdown strain, we uncovered its genome-wide but substrate-specific roles in C. neoformans splicing. The splicing functions of Prp16 are dependent on its helicase motif I and motif II that are conserved motifs for helicase activity. A small subset of introns spliced independent of Prp16 activity, were investigated to discover that exonic sequences at the 5 splice site (5SS) and 3 splice site (3SS) with stronger affinity for U5 loop 1 as a common feature in these introns. Furthermore, short (60-100nts) and ultra-short introns (<60nts) prevalent in the C. neoformans transcriptome were more sensitive to Prp16 knockdown than longer introns, indicating Prp16 is required for the efficient splicing of short and ultra-short introns. We propose that stronger U5 snRNA-pre-mRNA interactions enable the efficient transition of the spliceosome from the first to the second catalytic confirmation in Prp16 knockdown, particularly for short introns and introns with suboptimal features. This study provides insights into the fine-tuning spliceosomal helicase functions with variations in cis-element features.

molecular biology↗

bioRxiv2023

Cryptococcus neoformans Slu7 ensures nuclear positioning during mitotic progression through RNA splicing

The position of the nucleus before it divides during mitosis is variable in different budding yeasts. Studies in the pathogenic intron-rich fungus Cryptococcus neoformans reveal that the nucleus moves entirely into the daughter bud before its division. Here, we report functions of a zinc finger motif containing spliceosome protein C. neoformans Slu7 (CnSlu7) in cell cycle progression. The budding yeast and fission yeast homologs of Slu7 have predominant roles for intron 3 splice site definition during pre-mRNA splicing. Using a conditional knockdown strategy, we show CnSlu7 is an essential factor for viability and is required for efficient cell cycle progression with major role during mitosis. Aberrant nuclear migration, including improper positioning of the nucleus as well as the spindle, were frequently observed in cells depleted of CnSlu7. However, cell cycle delays observed due to Slu7 depletion did not activate the Mad2-dependent spindle assembly checkpoint (SAC). Mining of the global transcriptome changes in the Slu7 knockdown strain identified downregulation of transcripts encoding several cell cycle regulators and cytoskeletal factors for nuclear migration, and the splicing of specific introns of these genes was CnSlu7 dependent. To test the importance of splicing activity of CnSlu7 on nuclear migration, we complemented Slu7 knockdown cells with an intron less PAC1 minigene and demonstrated that the nuclear migration defects were significantly rescued. These findings show that CnSlu7 regulates the functions of diverse cell cycle regulators and cytoskeletal components, ensuring timely cell cycle transitions and nuclear division during mitosis.

microbiology↗

bioRxiv2023

Unequal genetic redundancy among the rice transcription factors OsMADS2 and OsMADS4 reveals distinct roles in floret organ development

Diversification of transcription factors and of their downstream targets can contribute to new organ morphologies. An example is rice lodicule, a small fleshy petal homolog that aids floret opening, thus facilitates pollination and fertility. To understand mechanisms underlying its specification, we investigated the developmental functions of the rice PISTILLATA (PI) paralogs, OsMADS2 and OsMADS4. Null osmads2 mutants reiterated OsMADS2 nonredundant lodicule specification roles and revealed new roles in flowering time and floral organ number and fate. Doubly perturbed osmads2d8/d8 osmads4kd florets had severe abnormalities, were female infertile, yet initiated parthenocarpy. Ubiquitous OsMADS4 overexpression rescued osmads2 abnormalities. Target genes whose regulation can contribute to OsMADS2 functions were discovered by its genome-wide binding analyses and transcriptome profiling. Several targets are implicated in lodicule and stamen development, floral organ number, cell wall, cell shape and osmotic homeostasis processes. Some targets relevant to lodicule development are cell division regulators (Cyclin D6, Cyclin P4-1-like), aquaporin (PIP1A), peptide transporter (PTR2), vascular development regulator (HOX1) and cell wall modulator (GH9B16). Their deregulation underscores the perturbed cell division, tissue differentiation patterns and physiology of the malformed osmads2 and osmads2d8/d8 osmads4kd lodicules. Altogether, we reveal novel roles for the rice PI paralogs in flowering time, panicle exsertion and embryo sac differentiation, divulge gene targets for lodicule development and provide mechanistic insights on the functional diversification of rice PI paralogs.

plant biology↗

bioRxiv2021

OsbZIP47 an integrator for meristem regulators during rice plant growth and development

Stem cell homeostasis by the WUS-CLV negative feedback loop is generally conserved across species; however, its links with other meristem regulators may have species-specific distinctions, rice being an example. We characterize rice OsbZIP47 for vegetative and inflorescence phenotypes in knockdown (OsbZIP47KD) transgenics and uncover its role in meristem maintenance and developmental progression. The shoot apical meristem (SAM) size in five day old OsbZIP47KD seedlings, was reduced as compared to the wild-type (WT). Whereas SAM in older twenty-five-day OsbZIP47KD plants was larger with increased size for L1 and underlying cells. We tested protein interactions of OsbZIP47 with other transcription factors and found partnerships with OsMADS1, RFL, and OSH1. Results from meta-analysis of deregulated panicle transcriptome datasets, in OsbZIP47KD, OsMADS1KD and RFLKD knockdown transgenics, and OSH1 genome-wide binding sites divulge potential targets coregulated by OsbZIP47, OsMADS1, OSH1 and RFL. Transcript analysis in OsbZIP47KD SAM and panicles showed abnormal gene expression for CLAVATA peptide-like signaling FON2-LIKE CLE PROTEIN1 (FCP1), FLORAL ORGAN NUMBER 2 (FON2), and hormone pathway: cytokinin (CK) Isopenteyltransferase2 (OsIPT2), Isopenteyltransferase8 (OsIPT8); auxin biosynthesis OsYUCCA6, OsYUCCA7; gibberellic acid (GA) biosynthesis GA20Ox1, GA20Ox4 and brassinosteriod biosynthesis CYP734A4 genes. The effects on ABBERANT PANICLE ORGANIZATION1 (APO1), OsMADS16, and DROOPING LEAF relate to second and third whorl organ phenotypes in OsbZIP47KD florets. Further, we demonstrate that OsbZIP47 redox status affects its DNA binding to cis elements in the FCP1 locus. Taken together, we provide insights on unique functional roles for OsbZIP47 in rice shoot meristem maintenance, its progression through inflorescence branching and floret development. One sentence summaryOsbZIP47 regulates rice shoot meristem size, panicle and floret development in concert with other meristem regulators such as OsMADS1, RFL and OSH1.

plant biology↗