Finding Correlations Between mRNA and Protein Levels in Leishmania Development: Is There a Discrepancy?

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.

Keywords: amastigote differentiation; gene expression; life cycle; metacyclogenesis; proteome; transcriptome.

Figure 1

Leishmania life cycle in mammalian and insect hosts. The differentiation processes involve drastic changes in pH, temperature, and nutrient availability, challenging the parasite’s ability to orchestrate its gene expression accordingly. Metacyclogenesis is essentially represented in the right portion of the figure, comprising the differentiation from procyclic into nectomonad and then into leptomonad and metacyclic forms inside the sandfly digestive tract. Amastigogenesis is represented in the left portion of the figure, comprising the differentiation from metacyclic promastigote to amastigote forms inside the mammalian host macrophage. N, Macrophage Nucleus; PV, Parasitophorous Vacuole.

Figure 2

Graph showing the number of publications retrieved in PubMed using the terms “mRNA AND leishmania” (light blue bars), “protein AND leishmania” (red bars), “transcriptome AND leishmania” (dark blue bars), “proteome AND leishmania” (pink bars), “transcriptomic AND leishmania” (gray bars), and “proteomic AND leishmania” (purple bars). The searches were conducted up to December 2021.

Figure 3

Main aspects of polycistronic and monocistronic gene expression. (A) Monocistronic coding regions are common to most higher eukaryotes. With this genome organization, protein-coding genes are organized within intronic portions that are nonprotein-coding regions. Transcription is regulated by promoters and enhancers; thus, transcription is individually controlled. Processing of precursor mRNA involves the removal of introns, 5’ cap addition and polyadenylation, generating the mature mRNA molecule that is translated after export from the nucleus. (B) The polycistronic organization of coding genes differentiates Leishmania gene expression. The absence of transcriptional control is shown, with several genes encoded in the same polycistronic coding region being transcribed together. Another difference is the existence of multicopy genes in tandem arrays. All these characteristics point to uncontrolled transcription. Processing of precursor mRNA involves trans-splicing (addition of the SL molecule), polyadenylation and RNAse activity to eliminate mRNAs that will not be translated.

Figure 4

Differentially expressed genes and proteins observed in independent transcriptomic and proteomic studies of Leishmania life cycle. Both Venn Diagrams on the top portion of the figure describe the total number of DEPs and DEGs found in all the analyzed studies that was based this review. Further, among the commonly differentially expressed genes, we indicate the amount of genes that presented correlation between mRNA and protein levels in metacyclogenesis and amastigogenesis. It is worth noting that these results should be read as proof-of-concept, since no statistical analysis was performed to compare the analyzed studies.