The identification of RNAs that are not translated into proteins was an important breakthrough, defining the diversity of molecules involved in eukaryotic regulation of gene expression. These non-coding RNAs can be divided into two main classes according to their length: short non-coding RNAs, such as microRNAs (miRNAs), and long non-coding RNAs (lncRNAs). The lncRNAs in association with other molecules can coordinate several physiological processes and their dysfunction may impact in several pathologies, including cancer and infectious diseases. They can control the flux of genetic information, such as chromosome structure modulation, transcription, splicing, messenger RNA (mRNA) stability, mRNA availability, and post-translational modifications. Long non-coding RNAs present interaction domains for DNA, mRNAs, miRNAs, and proteins, depending on both sequence and secondary structure. The advent of new generation sequencing has provided evidences of putative lncRNAs existence; however, the analysis of transcriptomes for their functional characterization remains a challenge. Here, we review some important aspects of lncRNA biology, focusing on their role as regulatory elements in gene expression modulation during physiological and disease processes, with implications in host and pathogens physiology, and their role in immune response modulation.

Evidence of Leishmania infection was found in small mammals captured between 1996 and 2000 in the Amaraji region, Pernambuco State, Brazil. The kDNA polymerase chain reaction (PCR), using primers specific for subgenus L. (Viannia), was positive for 43/153 water rats (Nectomys squamipes), 13/81 black rats (Rattus rattus), 15/103 grass mice (Bolomys lasiurus), 1/14 marsh mice (Holochilus scieurus), 2/50 field mice (Akodon arviculoides), 2/12 woolly opossums (Marmosa sp.), and 5/37 common opossums (Didelphis albiventris). This same kDNA PCR was positive for 12/61 dog and 8/58 horse skin samples. In paired PCR tests of 203 small mammals, 18.7% were positive with the kDNA primers and 18.2% with rDNA primers. Amastigotes were seen in 26/460 and L. (V.) braziliensis was isolated from 5 grass mice and 1 black rat. We concluded that small mammals, particularly rodents, are infected with parasites of the subgenus L. (Viannia). The isolation of L. (V.) braziliensis zymodeme IOC/Z74 from 6 rodents and the fact that all the other described L. (Viannia) species that commonly infect humans have never been found in rodents or marsupials leads us to suggest that the positive PCRs indicate infections of L. (V.) braziliensis. The isolation of zymodeme IOC/Z74 from humans reinforces our hypothesis that small, ground-loving mammals, such as rodents are the primary reservoirs of L. (V.) braziliensis.

We demonstrate that during inflammatory responses the nuclear factor kappa B (NF-κB) induces the synthesis of melatonin by macrophages and that macrophage-synthesized melatonin modulates the function of these professional phagocytes in an autocrine manner. Expression of a DsRed2 fluorescent reporter driven by regions of the aa-nat promoter, that encodes the key enzyme involved in melatonin synthesis (arylalkylamine-N-acetyltransferase), containing one or two upstream κB binding sites in RAW 264.7 macrophage cell lines was repressed when NF-κB activity was inhibited by blocking its nuclear translocation or its DNA binding activity or by silencing the transcription of the RelA or c-Rel NF-κB subunits. Therefore, transcription of aa-nat driven by NF-κB dimers containing RelA or c-Rel subunits mediates pathogen-associated molecular patterns (PAMPs) or pro-inflammatory cytokine-induced melatonin synthesis in macrophages. Furthermore, melatonin acts in an autocrine manner to potentiate macrophage phagocytic activity, whereas luzindole, a competitive antagonist of melatonin receptors, decreases macrophage phagocytic activity. The opposing functions of NF-κB in the modulation of AA-NAT expression in pinealocytes and macrophages may represent the key mechanism for the switch in the source of melatonin from the pineal gland to immune-competent cells during the development of an inflammatory response.

Leishmania (Leishmania)amazonensisis an intracellular protozoan parasite responsible for the cutaneous leishmaniasis. The parasite replicates inside mammalian macrophage to establish infection. Host-pathogen interactions result in microRNA-mediated post-transcriptional regulation of host genes involved in inflammatory immune response. We analyzed macrophage miRNA profiles duringL. (L.)amazonensisinfection. The regulation of macrophage miRNA expression by the parasite correlates with/depends on parasite arginase activity during infection.L. (L.)amazonensis (La-WT) presented significant miRNA profile alteration (27%) compared toL. (L.)amazonensisarginase knockout (La-arg⁻) (~40%) in relation to uninfected-macrophages. We observed that 78% of the altered miRNAs were up-regulated inLa-WT infection, while only 32% were up-regulated inLa-arg⁻-infected macrophages. In contrast toLa-WT, the lack ofL. (L.)amazonensisarginase led to the inhibition of miR-294 and miR-721 expression. The expression of miR-294 and miR-721 was recovered to levels similar toLa-WT inLa-arg⁻addback mutant. The inhibition of miR-294/Nos2 and miR721/Nos2interactions increased NOS2 expression and NO production, and reducedL. (L.)amazonensisinfectivity, confirmingNos2as target of these miRNAs. The role of miR-294 and miR-721 in the regulation of NOS2 expression duringLeishmaniareplication in infected macrophages pointing these miRNAs as potential new targets for drug development.

In Leishmania, de novo polyamine synthesis is initiated by the cleavage of L-arginine to urea and L-ornithine by the action of arginase (ARG, E.C. 3.5.3.1). Previous studies in L. major and L. mexicana showed that ARG is essential for in vitro growth in the absence of polyamines and needed for full infectivity in animal infections. The ARG protein is normally found within the parasite glycosome, and here we examined whether this localization is required for survival and infectivity. First, the localization of L. amazonensis ARG in the glycosome was confirmed in both the promastigote and amastigote stages. As in other species, arg⁻ L. amazonensis required putrescine for growth and presented an attenuated infectivity. Restoration of a wild type ARG to the arg⁻ mutant restored ARG expression, growth and infectivity. In contrast, restoration of a cytosol-targeted ARG lacking the glycosomal SKL targeting sequence (argΔSKL) restored growth but failed to restore infectivity. Further study showed that the ARGΔSKL protein was found in the cytosol as expected, but at very low levels. Our results indicate that the proper compartmentalization of L. amazonensis arginase in the glycosome is important for enzyme activity and optimal infectivity. Our conjecture is that parasite arginase participates in a complex equilibrium that defines the fate of L-arginine and that its proper subcellular location may be essential for this physiological orchestration.