About
77
Publications
9,596
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
2,262
Citations
Publications
Publications (77)
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 Slu...
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 Slu...
Functional diversification of transcription factors and of their downstream targets contributes to the emergence of new organ morphologies. To better understand the molecular mechanisms underlying floral organ specification in rice, we investigated the function of OsMADS2 and OsMADS4 , the rice PISTILLATA ( PI ) paralogs controlling lodicule and st...
Stem cell homeostasis by the WUSCHEL–CLAVATA (WUS-CLV) feedback loop is generally conserved across species; however, its links with other meristem regulators can be species-specific, rice being an example. We characterized the role of rice OsbZIP47 in vegetative and reproductive development. The knockdown (KD) transgenics showed meristem size abnor...
Main conclusion
A new, stable, null mutant of OsMADS1 generated by homologous recombination-based gene targeting in an indica rice confirms its regulatory role for floral meristem identity, its determinate development and floral organ differentiation.
Abstract
OsMADS1, an E-class MADS-box gene, is an important regulator of rice flower development....
Prp16 is a DEAH box pre-mRNA splicing factor that triggers a key spliceosome conformational switch to facilitate second step splicing in Saccharomyces cerevisiae. However, Prp16 functions are largely unexplored in Schizosaccharomyces pombe, an attractive model with exon-intron architecture more relevant to several other eukaryotes. Here, we generat...
Budding yeast spliceosomal factors ScSlu7 and ScPrp18 interact and mediate intron 3’ss choice during second step pre-mRNA splicing. The fission yeast genome with abundant multi-intronic transcripts, degenerate splice signals and SR proteins is an apt unicellular fungal model to deduce roles for core spliceosomal factors in alternative splice-site c...
Determination of identity corresponding to various cDNA products of ats1+ E2-I2-E3-I3-E4 by sequence analysis.
(A) Exon intron architecture of ats1+ E2-I2-E3-I3-E4 minigene driven by heterologous tbp1 promoter cloned in pDBlet shuttle vector (exon and intron sizes in nts are indicated in brackets). (B) Tracer labelled semi-quantitative RT-PCR analy...
(A) Western blotting analysis of SpSlu7 levels in cell lysates of slu7-2 strain grown in the presence and absence of thiamine using SpSlu7 polyclonal antisera (1:2500) as described in the Materials and methods. Coomassie-stained gel post-transfer serves as the loading control. (B) In vivo splicing analysis of tfIId+ intron 1 in the RNA samples of W...
Expression of marker genes to validate response to environmental stresses.
(A, B) Semi-quantitative analysis of transcript levels of hsp16+, a heatshock responsive gene, at varying time points of both strong (42°C) and mild (39°C) thermal stress. Splicing status of intron 1 of constitutively expressed tfIId+ transcript. act1+ transcript served as t...
Quantification of the various splice forms of ats1+ and DUF3074 in response to environmental stresses.
(A, B) Data from the densitometric analysis of various isoforms of ats1+ in slu7+ O/E, slu7-2, WT and prp18-5 cells subjected to mild thermal stress as shown in Fig 6A was plotted as bar graphs. The p value was calculated by unpaired student’s t t...
List of twenty custom-designed probes to detect alternate mRNA isoforms arising from altered use of splice sites.
In order to detect the ten isoforms formed due to the utilisation of altered 5’ss (donors) or 3’ss (acceptors) each, as reported in [16], twenty probe sequences were custom designed and incorporated in the SpPrp18 microarray platform [3...
(A) Flowchart summarizing the strategy adopted to identify exon skipping events consistently observed in wild-type cells from splicing microarray and different RNA sequencing datasets. (B) Methodology adopted to choose candidates and experimentally verify the use of non-canonical/alternative splice sites in these transcripts.
(TIF)
Heavy metal stress-specific effects on alternative splicing.
Effect of heavy metal stress on alternative and constitutive splicing of ats1+ E2-I2-E3-I3-E4 wild-type minitranscript. The analyses were performed in RNA from slu7+ O/E, slu7-2, WT and prp18-5 exposed to 0.5 mM CdS04 (as detailed in Materials and methods). Intronless act1+ is used as nor...
Oligonucleotides used for the study.
(DOCX)
List of 104 exon skipping events in wild-type fission yeast cells identified from the publically available NGS transcriptome data.
The exon skipping events were identified using the alternate splice junction probes used in splicing-sensitive microarray platform. The sequence reads corresponding to these junctions in the two NGS transcriptome data [...
Relative abundance of alternative splice isoforms in some RNA surveillance mutants.
(A) Wild-type Fy527, NMD mutant upf1Δ, exosome mutant dis3-54 strains were grown at 30°C. Constitutive and alternative splicing profile of ats1+ E2-I2-E3-I3-E4 minigene were assessed by semi-quantitative radiolabelled RT-PCR assays using T7 primer to selectively det...
The fission yeast genome which contains numerous short introns is an apt model for studies on fungal splicing mechanisms and splicing by intron-definition. Here we perform a domain analysis of the evolutionarily conserved Schizosaccharomyces pombe pre-mRNA processing factor, SpPrp18. Our mutational and biophysical analyses of the C- terminal alpha-...
OsMADS1 controls rice (Oryza sativa) floral fate and organ development. Yet, its genome-wide targets and the mechanisms underlying its role as a transcription regulator controlling developmental gene expression are unknown. We identify 3112 gene-associated OsMADS1-bound sites in the floret genome. These occur in the vicinity of transcription start...
Saccharomyces cerevisiae Sub1 is involved in several cellular processes such as, transcription initiation, elongation, mRNA processing and DNA repair. It has also been reported to provide cellular resistance during conditions of oxidative DNA damage and osmotic stress. Here, we report a novel role of SUB1 during starvation stress-induced sporulatio...
Studies on pre-mRNA splicing in fission yeast allows to examine diversity in the dynamics of
this gene regulatory process as intronic cis features bear resemblance to higher eukaryotic
genomes and are typical of other fungal and plant genomes. Here, we present functional studies
on spprp16+, an essential DEXH motif containing ATP dependent RN...
Axillary meristems (AMs) are secondary shoot meristems whose outgrowth determines plant architecture. In rice, AMs form tillers, and tillering mutants reveal an interplay between transcription factors and the phytohormones auxin and strigolactone as some factors that underpin this developmental process. Previous studies showed that knockdown of the...
The Polycomb Repressive Complex 2 (PRC2) represses transcriptional activity of target genes through trimethylation of Lysine 27 of Histone H3. The functions of the plant PRC2 have been chiefly described in Arabidopsis but specific functions in other plant species, especially the cereals, are still largely unknown. Here we characterize mutants in th...
Yeast Rpb4, a subunit of RNA pol II is not essential for viability but is involved in multiple cellular phenotypes such as temperature sensitivity, enhanced pseudohyphal morphology, and decreased sporulation. Both in vivo and in vitro studies strongly support involvement of Rpb4 in transcription initiation, while its role in transcription elongatio...
The multiple short introns in Schizosaccharomyces pombe genes with degenerate cis sequences and atypically positioned polypyrimidine tracts make an interesting model to investigate canonical and alternative
roles for conserved splicing factors. Here we report functions and interactions of the S. pombe slu7+ (spslu7+) gene product, known from Saccha...
SEPALLATA MADS-box transcription factors mediate floral development in association with other regulators. Mutants in five rice (Oryza sativa) SEP genes suggest both redundant and unique functions in panicle branching and floret development. LHS1/OsMADS1, from a grass-specific sub-group of LOFSEP genes, is required for specifying a single floret on...
Large numbers of Plasmodium genes have been predicted to have introns. However, little information exists on the splicing mechanisms in this organism. Here, we describe the DExD/DExH-box containing Pre-mRNA processing proteins (Prps), PfPrp2p, PfPrp5p, PfPrp16p, PfPrp22p, PfPrp28p, PfPrp43p and PfBrr2p, present in the Plasmodium falciparum genome a...
The yeast Bud31 protein, a Prp19 complex (NTC) member, aids spliceosome assembly and thus promotes efficient pre-mRNA splicing. The bud31 null cells show mild budding abnormalities at optimal growth temperatures and, at higher temperatures, have growth defects with aberrant budding. Here we have assessed cell cycle transitions which require Bud31....
Pre-mRNA splicing occurs in spliceosomes whose assembly and activation are critical for splice site selection and catalysis. The highly conserved NineTeen complex protein complex stabilizes various snRNA and protein interactions early in the spliceosome assembly pathway. Among several NineTeen complex-associated proteins is the nonessential protein...
GH3 proteins control auxin homeostasis by inactivating excess auxin as conjugates of amino acids and sugars and thereby controlling cellular bioactive auxin. Since auxin regulates many aspects of plant growth and development, regulated expression of these genes offers a mechanism to control various developmental processes. OsMGH3/OsGH3-8 is express...
In Arabidopsis thaliana, a eudicot species, the transcription factor LFY is expressed throughout the floral meristem and promotes their formation. The expression pattern of the rice LFY homolog-RFL shows distinct differences from that of its Arabidopsis counterpart. In the March issue of PNAS (2008) we have shown the temporally-regulated high-level...
Saccharomyces cerevisiae PRP17-null mutants are temperature-sensitive for growth. In vitro splicing with extracts lacking Prp17 are kinetically slow for the first step of splicing and are arrested for the second step at temperatures greater than 34 degrees C. In the present study we show that these stalled spliceosomes are compromised for an essent...
The SEPALLATA genes encode a functionally diverse group of MADS
domain transcription factors including redundant floral organ fate
determinants in Arabidopsis and non-redundant factors like OsMADS1
in rice. Earlier functional studies show that OsMADS1 regulates the
identity of all floret organs and controls floret meristem determinacy.
To investiga...
Activity of axillary meristems dictates the architecture of both vegetative and reproductive parts of a plant. In Arabidopsis thaliana, a model eudicot species, the transcription factor LFY confers a floral fate to new meristems arising from the periphery of the reproductive shoot apex. Diverse orthologous LFY genes regulate vegetative-to-reproduct...
Functional diversification of duplicated genes can contribute to the emergence of new organ morphologies. Model eudicot plants like Arabidopsis thaliana and Antirrhinum majus have a single PI/GLO gene that together with AP3/DEF regulate petal and stamen formation. Lodicules of grass flowers are morphologically distinct reduced organs occupying the...
A combination of environmental factors and endogenous cues trigger floral meristem initiation on the flanks of the shoot meristem. A plethora of regulatory genes have been implicated in this process. They function either as activators or as repressors of floral initiation. This review describes the mode of their action in a regulatory network that...
Grass flowers are highly derived compared to their eudicot counterparts. To delineate OsMADS1 functions in rice floret organ development we have examined its evolution and the consequences of its knockdown or overexpression. Molecular phylogeny suggests the co-evolution of OsMADS1 with grass family diversification. OsMADS1 knockdown perturbs the di...
Removal of pre-mRNA introns is an essential step in eukaryotic genome interpretation. The spliceosome, a ribonucleoprotein performs this critical function; however, precise roles for many of its proteins remain unknown. Genome-wide consequences triggered by the loss of a specific factor can elucidate its function in splicing and its impact on other...
A review. Understanding mechanisms that regulate when, where and how flowers are formed will provide insights into the control of cell-fate detn. in plants. Flowering in higher plants is regulated by both genetic and environmental factors, and culminates in formation of specialized organs, specific to the flower, which are patterned in a species-sp...
Unlike many eudicot species, grasses have duplicated PI/GLO-like genes. Functional analysis of one of the rice PI/GLO paralogs, OsMADS2, is reported here. Our data demonstrate its essential role in lodicule development and implicate the second PI/GLO paralog, OsMADS4, to suffice for stamen specification. We provide the first evidence for differenti...
Saccharomyces cerevisiaePRP17 (CDC40) encodes a second‐step pre‐mRNA splicing factor with a role in cell division. The functions of Prp17 in specific cell cycle
transitions were examined using temperature‐sensitive alleles in arrest/release experiments. We find that G1/S and G2/M transitions depend on Prp17. G1‐synchronized prp17::LEU2 cells arrest...
LFY and its orthologues are necessary for flower specification in diverse dicotyledonous plants. The spatial and temporal RNA expression pattern of a rice LFY-like gene: RFL differs significantly from that in several other species studied thus far. The onset of RFL expression coincides with inflorescence meristem (panicle meristem) initiation, and...
MADS-domain-containing transcription factors play diverse roles in plant development. The prototypic members of this gene family are the floral organ identity genes of the model dicotyledonous plant, Arabidopsis thaliana. Sequence relatedness and function ascribe them to AP1/AGL9, AG, AP3 and PI gene groups. The rice MADS-box gene, OsMADS1, is a me...
Understanding mechanisms that regulate when, where and how flowers are formed would elucidate cell-fate determination in plants. Some of the ad- vances made towards deciphering genes controlling floral induction, meristem specification and floral organ patterning are reviewed here. Studies begin- ning in the early 1980s of mutations in Arabidopsis...
In Saccharomyces cerevisiae, Prp17p is required for the efficient completion of the second step of pre-mRNA splicing. The function and interacting factors for this protein have not been elucidated. We have performed a mutational analysis of yPrp17p to identify protein domains critical for function. A series of deletions were made throughout the reg...
To unravel gene expression patterns during rice inflorescence development, particularly at early stages of panicle and floral organ specification, we have characterized random cloned cDNAs from developmental-stage-specific libraries. CDNA libraries were constructed from rice panicles at the stage of branching and flower primordia specification or f...
Studies of floral organ development in two dicotyledonous plants, Arabidopsis thaliana and Antirrhinum majus, have shown that three sets of genes (A, B and C) can pattern sepals, petals, stamens and carpels [1,2]. Mechanisms that define boundaries between these floral whorls are unclear, however. The Arabidopsis gene SUPERMAN (SUP), which encodes a...
Earlier studies on genetic suppression ofprp24-1 byprp21-2 suggested an association between yeast Prp21 and Prp24 proteins, which are associated, respectively, with U2 snRNA and U6
snRNA. Here we report analyses of physical and functional interaction between these factors. Missense mutations in functionally
important domains reside inprp21-2 andprp...
The PRP17 gene product is required for the second step of pre-mRNA splicing reactions. The C-terminal half of this protein bears four repeat units with homology to the beta transducin repeat. Missense mutations in three temperature-sensitive prp17 mutants map to a region in the N-terminal half of the protein. We have generated, in vitro, 11 missens...
Flower development provides a model system to study mechanisms that govern pattern formation in plants. Most flowers consist
of four organ types that are present in a specific order from the periphery to the centre of the flower. Reviewed here are
studies on flower development in two model species:Arabidopsis thaliana andAntirrhinum majus that focu...
The temperature-sensitive prp24-1 mutation defines a gene product required for the first step in pre-mRNA splicing. PRP24 is probably a component of the U6 snRNP particle. We have applied genetic reversion analysis to identify proteins that interact with PRP24. Spontaneous revertants of the temperature-sensitive (ts)prp24-1 phenotype were analyzed...
The products ofPRP17 andPRP18 genes are required for the second step of pre-mRNA splicing reactions inSaccharomyces cerevisiae. Temperature-sensitive mutants at either of these loci accumulate products of the first splicing reaction at nonpermissive
temperature. To characterize functional regions in these proteins the mutations in three temperature...
The apetala1 mutation of Arabidopsis affects floral meristem identity and the development of sepal and petal primordia of the flower. We mapped the available RFLP markers on chromosome 1 that are in the general vicinity of apetala1 on a fine structure map and then chose the closest RFLP as a starting point for contiguous DNA (contig) generation. We...
We report on the characterization of the yeast prp20-1 mutant. In this temperature-sensitive mutant, multiple steps of mRNA metabolism are affected. The prp20-1 mutant strain showed alterations in mRNA steady-state levels, defective mRNA splicing and changes in transcription initiation or termination when shifted from the permissive to the non-perm...
We have isolated a yeast mutant, ts352, that is temperature-sensitive for growth. The mutation has a general effect on mRNA metabolism and a specific effect on tRNA biosynthesis. Cells shifted to the nonpermissive temperature accumulate tRNAs that are shorter than mature tRNAs. The increased ability of these tRNAs to accept ATP demonstrates that gr...
In an effort to identify genes involved in the excision of tRNA introns in Saccharomyces cerevisiae, temperature-sensitive mutants were screened for intracellular accumulation of intron-containing tRNA precursors by RNA hybridization analysis. In one mutant, tRNA splicing intermediates consisting of the 5' exon covalently joined to the intron ('2/3...
We have investigated the role of a novel temperature-sensitive splicing mutation, prp18. We had previously demonstrated that
an accumulation of the lariat intermediate of splicing occurred at the restrictive temperature in vivo. We have now used the
yeast in vitro splicing system to show that extracts from this mutant strain are heat labile for the...
We have investigated the role of a novel temperature-sensitive splicing mutation, prp18. We had previously demonstrated that an accumulation of the lariat intermediate of splicing occurred at the restrictive temperature in vivo. We have now used the yeast in vitro splicing system to show that extracts from this mutant strain are heat labile for the...
In this study we report the isolation of temperature-sensitive mutants that affect pre-mRNA splicing. A bank of approximately 1000 temperature-sensitive Saccharomyces cerevisiae strains was generated and screened on RNA gel blots by hybridization with an actin intron probe. We isolated 16 mutants defining 11 new complementation groups prp(rna)17-pr...
The removal of introns from the primary transcript occurs by RNA splicing. Three major types of RNAs; tRNA, rRNA and mRNA, are known to contain introns. There are two general questions concerning any splicing mechanism: first, how is the precise recognition and alignment of the splice junctions achieved in introns whose lengths vary from a few hund...
The removal of introns from the primary transcript occurs by RNA splicing. Three major types of RNAs: tRNA, rRNA and mRNA, are known to contain introns. There are two general questions concerning any splicing mechanism: first, how is the precise recognition and alignment of the splice junctions achieved in introns whose lengths vary from a few hund...
Yeast introns contain three highly conserved sequences which are known to be required for splicing of pre-mRNA. Using in vitro mutagenesis, we have synthesized seven point mutations at five different sites in these signals in the yeast actin intron. The mutant introns were then inserted into each of three constructs, which allowed us to assess the...
splicing mutation, prpl8. We hadpreviously demonstrated that anaccumulation ofthelariat intermediate ofsplicing occurred attherestrictive temperature invivo. Wehavenow usedtheyeastinvitro splicing systemtoshowthat extracts fromthis mutantstrain are heat labile forthesecond reaction ofsplicing. Theheatinactivation ofprpl8extracts results fromloss of...
