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Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA.

ABSTRACT: Trypanosomatids are protozoan parasites and the causative agent of infamous infectious diseases. These organisms regulate their gene expression mainly at the post-transcriptional level and possess characteristic RNA processing mechanisms. In this study, we analyzed the complete repertoire of Leishmania major small nucleolar (snoRNA) RNAs by performing RNA-seq analysis on RNAs that were affinity-purified using the C/D snoRNA core protein, SNU13, and the H/ACA core protein, NHP2. This study revealed a large collection of C/D and H/ACA snoRNAs, organized in gene clusters generally containing both snoRNA types. Abundant snoRNAs were identified and predicted to guide trypanosome-specific rRNA cleavages. The repertoire of snoRNAs was compared to that of the closely related Trypanosoma brucei, and 80% of both C/D and H/ACA molecules were found to have functional homologues. The comparative analyses elucidated how snoRNAs evolved to generate molecules with analogous functions in both species. Interestingly, H/ACA RNAs have great flexibility in their ability to guide modifications, and several of the RNA species can guide more than one modification, compensating for the presence of single hairpin H/ACA snoRNA in these organisms. Placing the predicted modifications on the rRNA secondary structure revealed hypermodification regions mostly in domains which are modified in other eukaryotes, in addition to trypanosome-specific modifications.

SUBMITTER: Eliaz D

PROVIDER: S-EPMC4829279 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA.

Eliaz Dror D Doniger Tirza T Tkacz Itai Dov ID Biswas Viplov Kumar VK Gupta Sachin Kumar SK Kolev Nikolay G NG Unger Ron R Ullu Elisabetta E Tschudi Christian C Michaeli Shulamit S

RNA biology 20150513 11

Trypanosomatids are protozoan parasites and the causative agent of infamous infectious diseases. These organisms regulate their gene expression mainly at the post-transcriptional level and possess characteristic RNA processing mechanisms. In this study, we analyzed the complete repertoire of Leishmania major small nucleolar (snoRNA) RNAs by performing RNA-seq analysis on RNAs that were affinity-purified using the C/D snoRNA core protein, SNU13, and the H/ACA core protein, NHP2. This study reveal ...[more]

PMID: 25970223

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Project description:Although the nucleolus is known to be involved in the plant stress response, the underlying mechanisms remain unclear. In the present study, we genetically isolated and characterized the Arabidopsis thaliana salt hypersensitive mutant 1 (sahy1), which exhibits slow growth, short roots, and sterility. SAHY1 encodes an unknown protein that is predominantly expressed in root tips and mature pollens. Subcellular localization further demonstrated that SAHY1 is a nucleolar protein. Ploidy analysis and detection of S-phase cell cycle progression indicated that mitosis is reduced in the root tips of sahy1 plants. Furthermore, levels of reactive oxygen species (ROS) are reduced in the mutant. In addition to exhibiting changes in venation pattern, palisade mesophyll cells, the auxin response, and fertility, the sahy1 mutant is resistant to the protein translation inhibitors, streptomycin and cycloheximide, and has altered expression profiles of ribosome-related genes, reflecting the involvement of SAHY1 in ribosome assembly. Using a combination of transcriptome and gene coexpression clustering analyses, we identified a striking functional module in which SPIRAL 1-LIKE 4 (SPL4), which encodes a microtubule-localized protein, mediates the salt response that acts by modulating dynamic microtubule instability. Supporting evidence indicates that sahy1 is resistant to a microtubule-destabilizing drug (oryzalin), that the cortical microtubule array in sahy1 exhibits changes in dynamic instability, and that the spr1/spl2/spl3/spl4 quadruple mutant is oversensitive to salt. Collectively, these data demonstrate that a novel nucleolar protein, SAHY1, plays critical roles in salt sensitivity, plant growth, and development by integrating the diverse functions of its downstream genes. As the sahy1 mutant plants showed slow growth, short roots, and sterility, the aim of this experiment is to examine gene expression profile in root tissues mediated by SAHY1. The data obtained from this study was compared with chip database derived from root tissues and performed an analysis of gene coexpression clustering.

Dataset Information

Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA.

Publications

Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA.

Similar Datasets

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