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Borges FS, Quilles JC, Lorenzon LB, Espada CR, Freitas-Castro F, Defina TPA, Holetz FB, Cruz AK. Leishmania Ribosomal Protein (RP) paralogous genes compensate each other's expression maintaining protein native levels. PLoS One 2024; 19:e0292152. [PMID: 38753846 PMCID: PMC11098316 DOI: 10.1371/journal.pone.0292152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
In the protozoan parasite Leishmania, most genes encoding for ribosomal proteins (RPs) are present as two or more copies in the genome. However, their untranslated regions (UTRs) are predominantly divergent and might be associated with a distinct regulation of the expression of paralogous genes. Herein, we investigated the expression profiles of two RPs (S16 and L13a) encoded by duplicated genes in Leishmania major. The genes encoding for the S16 protein possess identical coding sequences (CDSs) and divergent UTRs, whereas the CDSs of L13a diverge by two amino acids and by their UTRs. Using CRISPR/Cas9 genome editing, we generated knockout (Δ) and endogenously tagged transfectants for each paralog of L13a and S16 genes. Combining tagged and Δ cell lines we found evidence of differential expression of both RPS16 and RPL13a isoforms throughout parasite development, with one isoform consistently more abundant than its respective copy. In addition, compensatory expression was observed for each paralog upon deletion of the corresponding isoform, suggesting functional conservation between these proteins. This differential expression pattern relates to post-translational processes, given compensation occurs at the level of the protein, with no alterations detected at transcript level. Ribosomal profiles for RPL13a indicate a standard behavior for these paralogues suggestive of interaction with heavy RNA-protein complexes, as already reported for other RPs in trypanosomatids. We identified paralog-specific bound to their 3'UTRs which may be influential in regulating paralog expression. In support, we identified conserved cis-elements within the 3'UTRs of RPS16 and RPL13a; cis-elements exclusive to the UTR of the more abundant paralog or to the less abundant ones were identified.
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Affiliation(s)
- Francisca S. Borges
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - José C. Quilles
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Lucas B. Lorenzon
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Caroline R. Espada
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Felipe Freitas-Castro
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Tânia P. A. Defina
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Fabíola B. Holetz
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Paraná, Brazil
| | - Angela K. Cruz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
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Cortazzo da Silva L, Aoki JI, Floeter-Winter LM. Finding Correlations Between mRNA and Protein Levels in Leishmania Development: Is There a Discrepancy? Front Cell Infect Microbiol 2022; 12:852902. [PMID: 35903202 PMCID: PMC9318571 DOI: 10.3389/fcimb.2022.852902] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/02/2022] [Indexed: 12/02/2022] Open
Abstract
Multiple genes and proteins have been identified as differentially expressed in the stages of the Leishmania life cycle. The differentiation processes are implicated in specific transcriptional and proteomic adjustments driven by gene expression regulation mechanisms. Leishmania parasites lack gene-specific transcriptional control, and gene expression regulation mostly depends on posttranscriptional mechanisms. Due to the lack of transcriptional regulation, criticism regarding the relevance of transcript quantification as a possible and efficient prediction of protein levels is recurrent in studies that use transcriptomic information. The advent of high-throughput technologies has improved the analysis of genomes, transcriptomes and proteomes for different organisms under several conditions. Nevertheless, defining the correlation between transcriptional and proteomic profiles requires arduous and expensive work and remains a challenge in Leishmania. In this review, we analyze transcriptomic and proteomic data for several Leishmania species in two different stages of the parasite life cycle: metacyclogenesis and amastigogenesis (amastigote differentiation). We found a correlation between mRNA and protein levels of 60.9% and 69.8% for metacyclogenesis and amastigogenesis, respectively; showing that majority mRNA and protein levels increase or decrease concomitantly. Among the analyzed genes that did not present correlation indicate that transcriptomic data should be carefully interpreted as protein expression. We also discuss possible explanations and mechanisms involved for this lack of correlation.
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Ruy PDC, Monteiro-Teles NM, Miserani Magalhães RD, Freitas-Castro F, Dias L, Aquino Defina TP, Rosas De Vasconcelos EJ, Myler PJ, Kaysel Cruz A. Comparative transcriptomics in Leishmania braziliensis: disclosing differential gene expression of coding and putative noncoding RNAs across developmental stages. RNA Biol 2019; 16:639-660. [PMID: 30689499 DOI: 10.1080/15476286.2019.1574161] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Leishmaniasis is a worldwide public health problem caused by protozoan parasites of the genus Leishmania. Leishmania braziliensis is the most important species responsible for tegumentary leishmaniases in Brazil. An understanding of the molecular mechanisms underlying the success of this parasite is urgently needed. An in-depth study on the modulation of gene expression across the life cycle stages of L. braziliensis covering coding and noncoding RNAs (ncRNAs) was missing and is presented herein. Analyses of differentially expressed (DE) genes revealed that most prominent differences were observed between the transcriptomes of insect and mammalian proliferative forms (6,576 genes). Gene ontology (GO) analysis indicated stage-specific enriched biological processes. A computational pipeline and 5 ncRNA predictors allowed the identification of 11,372 putative ncRNAs. Most of the DE ncRNAs were found between the transcriptomes of insect and mammalian proliferative stages (38%). Of the DE ncRNAs, 295 were DE in all three stages and displayed a wide range of lengths, chromosomal distributions and locations; many of them had a distinct expression profile compared to that of their protein-coding neighbors. Thirty-five putative ncRNAs were submitted to northern blotting analysis, and one or more hybridization-positive signals were observed in 22 of these ncRNAs. This work presents an overview of the L. braziliensis transcriptome and its adjustments throughout development. In addition to determining the general features of the transcriptome at each life stage and the profile of protein-coding transcripts, we identified and characterized a variety of noncoding transcripts. The novel putative ncRNAs uncovered in L. braziliensis might be regulatory elements to be further investigated.
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Affiliation(s)
- Patrícia De Cássia Ruy
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Natália Melquie Monteiro-Teles
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Rubens Daniel Miserani Magalhães
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Felipe Freitas-Castro
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Leandro Dias
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Tania Paula Aquino Defina
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | | | - Peter J Myler
- b Center for Infectious Disease Research , Seattle, Washington , USA
| | - Angela Kaysel Cruz
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
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