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Although several stage-specific genes have been identified in Leishmania, the molecular mechanisms governing developmental gene regulation in this organism are still not well understood. We have previously reported an attenuation of virulence in Leishmania major and L. braziliensis carrying extra-copies of the spliced leader RNA gene. Here, we surveyed the major differences in proteome and transcript expression profiles between the spliced leader RNA overexpressor and control lines using two-dimensional gel electrophoresis and differential display reverse transcription PCR, respectively. Thirty-nine genes related to stress response, cytoskeleton, proteolysis, cell cycle control and proliferation, energy generation, gene transcription, RNA processing and post-transcriptional regulation have abnormal patterns of expression in the spliced leader RNA overexpressor line. The evaluation of proteolytic pathways in the mutant revealed a selective increase of cysteine protease activity and an exacerbated ubiquitin-labeled protein population. Polysome profile analysis and measurement of cellular protein aggregates showed that protein translation in the spliced leader RNA overexpressor line is increased when compared to the control line. We found that L. major promastigotes maintain homeostasis in culture when challenged with a metabolic imbalance generated by spliced leader RNA surplus through modulation of intracellular proteolysis. However, this might interfere with a fine-tuned gene expression control necessary for the amastigote multiplication in the mammalian host.
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http://dx.doi.org/10.1016/j.biocel.2010.06.013 | DOI Listing |
Brief Bioinform
August 2025
Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
Spliced leader (SL) trans-splicing occurs in a wide range of eukaryotes and plays a critical role in processing mRNAs derived from operon structures. However, current research on this mechanism remains limited, partly due to the difficulty in accurately identifying genuine SL trans-splicing events. The advent of long-read RNA sequencing technologies, such as direct RNA sequencing by Oxford Nanopore Technologies, offers a more promising avenue for detecting these events with greater resolution.
View Article and Find Full Text PDFBMC Genomics
July 2025
Research Center in Infectious Diseases and Axis of Infectious and Immune Diseases, Research Center of the Centre Hospitalier Universitaire de Québec-Université Laval, 2705 Laurier Blvd, Quebec, QC, G1V 4G2, Canada.
Background: relies on posttranscriptional control to regulate gene expression. Protein-coding genes are synthesised as polycistronic precursors that are processed into individual mRNAs by -splicing adding the spliced leader (SL) RNA to the 5’-end and 3’ cleavage-polyadenylation. Here, we employ Nanopore direct RNA sequencing (DRS) combined with Illumina RNA-Seq to comprehensively interrogate the transcriptomes of developmental stages at single-molecule resolution.
View Article and Find Full Text PDFOpen Biol
April 2025
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
Retroposition is a gene duplication mechanism that uses RNA molecules as intermediaries to generate new gene copies. Dinoflagellates are proposed as an ideal model for exploring this process due to the tagging of retrogenes with DNA-encoded remnants of the dinoflagellate-specific splice-leader motif at their 5' end. We conducted a comprehensive search for retrogenes in dinoflagellate transcriptomes to uncover their functional nature and the processes underlying their redundancy.
View Article and Find Full Text PDFmBio
May 2025
Cell Cycle Laboratory, Butantan Institute, São Paulo, Brazil.
The protozoan is the causative agent of Chagas disease and is known for its polycistronic transcription, with about 50% of its genome consisting of repetitive sequences, including coding (primarily multigenic families) and non-coding regions (such as ribosomal DNA, spliced leader [SL], and retroelements, etc). Here, we evaluated the genomic features associated with higher-order chromatin organization in (Brazil A4 strain) by extensive computational processing of high-throughput chromosome conformation capture (Hi-C). Through the mHi-C pipeline, designed to handle multimapping reads, we demonstrated that applying canonical Hi-C processing, which overlooks repetitive DNA sequences, results in a loss of DNA-DNA contacts, misidentifying them as chromatin-folding (CF) boundaries.
View Article and Find Full Text PDFNucleic Acids Res
February 2025
Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, United States.
In all three domains of life, genes with related functions can be organized into specific genomic regions known as gene clusters. In eukaryotes, histone, piRNA (Piwi-interacting RNA), and rDNA (ribosomal DNA) clusters are among the most notable clusters which play fundamental roles in chromatin formation, genome integrity, and translation, respectively. These clusters have long been thought to be regulated by distinct transcriptional mechanisms.
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