Investigating the interference of single nucleotide polymorphisms with miRNA mediated gene regulation in pancreatic ductal adenocarcinoma: An in silico approach.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) has a strong genetic component and single nucleotide polymorphisms (SNPs) in key genes have been found to modulate the susceptibility of the individuals to the disease. SNPs in 3'-UTR of the target genes or in miRNA seed region has gained much importance as this may lead to impairment of miRNA-mRNA interaction. Not much information about this phenomenon is available with respect to PDAC and we wanted to predict such SNPs which could affect miRNA function in the disease using bioinformatics tools. METHODS: After identifying the deregulated miRNAs and genes in PDAC, we determined how many of those altered genes are among experimentally validated targets of those miRNAs. Subsequently, SNPs which could alter these miRNA-mRNA interactions were detected using multiple webtools following high stringent conditions. Disease relevance of the SNPs were also evaluated. RESULTS: We identified a total of 2492 experimentally validated target genes for 303 miRNAs deregulated in PDAC. Our meta-analysis from 363 PDAC patients and 162 control individuals resulted in a set of differentially expressed genes in pancreatic cancer, which was further compared with the miRNA target genes to get targets differentially expressed in pancreatic cancer. We further detected SNPs either in 'seed' region of miRNAs or 'seed-match' sequence of mRNAs either having disruption or creation of miRNA binding site, correlated the expression for each miRNA-SNP-mRNA interaction. Selected SNPs were found to be in LD with important GWAS identified SNPs. CONCLUSION: Our study, hereby, explores the probable effects of SNPs on miRNA-target mRNA interactions. Through stringent analytical methods, we have identified 3 common variants and 13other rare variants possibly interfering with miRNA mediated gene regulation in PDAC.

Identification of Key Deregulated RNA-Binding Proteins in Pancreatic Cancer by Meta-Analysis and Prediction of Their Role as Modulators of Oncogenesis.

RNA-binding proteins (RBPs) play a significant role in multiple cellular processes with their deregulations strongly associated with cancer. However, there are not adequate evidences regarding global alteration and functions of RBPs in pancreatic cancer, interrogated in a systematic manner. In this study, we have prepared an exhaustive list of RBPs from multiple sources, downloaded gene expression microarray data from a total of 241 pancreatic tumors and 124 normal pancreatic tissues, performed a meta-analysis, and obtained differentially expressed RBPs (DE-RBPs) using the Limma package of R Bioconductor. The results were validated in microarray datasets and the Cancer Genome Atlas (TCGA) RNA sequencing dataset for pancreatic adenocarcinoma (PAAD). Pathway enrichment analysis was performed using DE-RBPs, and we also constructed the protein-protein interaction (PPI) network to detect key modules and hub-RBPs. Coding and noncoding targets for top altered and hub RBPs were identified, and altered pathways modulated by these targets were also investigated. Our meta-analysis identified 45 upregulated and 15 downregulated RBPs as differentially expressed in pancreatic cancer, and pathway enrichment analysis demonstrated their important contribution in tumor development. As a result of PPI network analysis, 26 hub RBPs were detected and coding and noncoding targets for all these RBPs were categorized. Functional exploration characterized the pathways related to epithelial-to-mesenchymal transition (EMT), cell migration, and metastasis to emerge as major pathways interfered by the targets of these RBPs. Our study identified a unique meta-signature of 26 hub-RBPs to primarily modulate pancreatic tumor cell migration and metastasis in pancreatic cancer. IGF2BP3, ISG20, NIP7, PRDX1, RCC2, RUVBL1, SNRPD1, PAIP2B, and SIDT2 were found to play the most prominent role in the regulation of EMT in the process. The findings not only contribute to understand the biology of RBPs in pancreatic cancer but also to evaluate their candidature as possible therapeutic targets.

Bioinformatic Analysis and Integration of Transcriptome and Proteome Results Identify Key Coding and Noncoding Genes Predicting Malignancy in Intraductal Papillary Mucinous Neoplasms of the Pancreas.

BACKGROUND: Intraductal papillary mucinous neoplasms (IPMNs) are precursor lesions of pancreatic ductal adenocarcinoma (PDAC). IPMNs are generally associated with high risk of developing malignancy and therefore need to be diagnosed and assessed accurately, once detected. Existing diagnostic methods are inadequate, and identification of efficient biomarker capable of detecting high-risk IPMNs is necessitated. Moreover, the mechanism of development of malignancy in IPMNs is also elusive. METHODS: Gene expression meta-analysis conducted using 12 low-risk IPMN and 23 high-risk IPMN tissue samples. We have also listed all the altered miRNAs and long noncoding RNAs (lncRNAs), identified their target genes, and performed pathway analysis. We further enlisted cyst fluid proteins detected to be altered in high-risk or malignant IPMNs and compared them with fraction of differentially expressed genes secreted into cyst fluid. RESULTS: Our meta-analysis identified 270 upregulated and 161 downregulated genes characteristically altered in high-risk IPMNs. We further identified 61 miRNAs and 14 lncRNAs and their target genes and key pathways contributing towards understanding of the gene regulation during the progression of the disease. Most importantly, we have detected 12 genes altered significantly both in cystic lesions and cyst fluid. CONCLUSION: Our study reports, for the first time, a meta-analysis identifying key changes in gene expression between low-risk and high-risk IPMNs and also explains the regulatory aspect through construction of a miRNA-lncRNA-mRNA interaction network. The 12-gene-signature could function as potential biomarker in cyst fluid for detection of IPMN with a high risk of developing malignancy.

Circadian rhythm genes in cancer: insight into their functions and regulation involving noncoding RNAs.

The 24-h circadian rhythm handles a wide variety of physiological needs. Clock genes, in coordination with other tissue-specific factors regulate various processes and often turns responsible for the pathological conditions when altered. Cancer is one such disease where the clock genes have been shown to contribute at multiple levels modulating key hallmarks of cancer. Most importantly, adding to this complication, noncoding RNAs (ncRNAs) have emerged as one of the major post-transcriptional regulators of gene expression and many recent studies have indicated about involvement of microRNAs or long noncoding RNAs in the process. In this review, we have described how do circadian pathway genes participated in oncogenesis and also updated the latest status of ncRNA involvement. We also try to address the existing gaps to have a more comprehensive understanding of the phenomenon in future.Abbreviations: HIFs: hypoxia-inducible factors; VEGF: Vascular endothelial growth factor; Mdm2: Mouse double minute 2 homolog; ATM: Ataxia telangiectasia mutated; Chk2: Checkpoint kinase 2; Bcl-Xl: B-cell lymphoma-extra-large; Bcl-2: B-cell lymphoma 2; DGCR8: DiGeorge syndrome chromosomal region 8; PPAR-γ: Peroxisome proliferator-activated receptor gamma.

Noncoding RNAs as key modulators of autophagy in pancreatic cancer (Review).

Inability of early detection as well as lack of proper therapeutic intervention, both add to the complexity of pancreatic cancer. Understanding of the basic cellular processes is of the utmost importance and autophagy is one of these processes. Considering the importance of this process in normal cellular functions as well as in pathological states, elaboration of the updated information on the mechanism of autophagy was initially carried out. Autophagy is a process for degradation of damaged cellular organelles, abnormal proteins and even nutrients which happen via formation of autophagosomes. Incidentally, autophagy has been shown to play both oncogenic and tumour­suppressive functions in cancer and has also been shown to modulate stemness of cancer cells, recurrence and resistance to chemotherapeutic agents. The contribution of autophagy genes and pathways in pancreatic tumorigenesis was also evaluated. Regulation is the key step in any such cellular phenomenon and noncoding RNA­mediated regulation is an emerging field. While miRNAs participate mainly in post­transcriptional regulation, long noncoding RNAs and circular RNAs have more diverse regulatory functions. Noncoding RNAs are also shown to modulate both the tumour­promoting and tumour­suppressing functions of autophagy in pancreatic cancer. The implication of noncoding RNA­mediated regulation with respect to radio­resistance and chemo­resistance of pancreatic cancer cells was also assessed. To the best of our knowledge, this is the first ever attempt trying to decipher the cross­talk between autophagy­noncoding RNAs and genes involved in the development and progression of pancreatic cancer.

Pilot study identifying circulating miRNA signature specific to alcoholic chronic pancreatitis and its implication on alcohol-mediated pancreatic tissue injury.

BACKGROUND AND AIM: Alcohol exerts its effects on organs in multiple ways. Alcoholic chronic pancreatitis (ACP) is a disease in which alcohol triggers the pathological changes in pancreas, leading to chronic inflammation and fibrosis. The molecular mechanism behind these changes is not clear. Identification of key circulating miRNA changes in ACP patients and determination of the fraction that is secreted from diseased pancreas not only could serve as potential biomarker for assessing disease severity, but also could help identifying the molecular alterations prevailing in the organ precipitating the disease, to some extent. METHODS: We performed microRNA microarray using the Affymetrix miRNA 4.0 platform to identify differentially expressed miRNAs in serum of ACP patients as compared to alcoholic control individuals and then found out how many of them could be pancreas-specific and exosomally secreted. We further analyzed a pancreatitis-specific gene expression data set to find out the differentially expressed genes in diseased pancreas and explored the possible role of those selected miRNAs in regulation of gene expression in ACP. RESULTS: We identified 14 miRNAs differentially expressed in both serum and pancreas and also identified their experimentally validated targets. Transcription factors modulating the miRNA expression in an alcohol-dependent manner were also identified and characterized to derive the miRNA-gene-TF interaction network responsible for progression of the disease. CONCLUSIONS: Differentially expressed miRNA signature demonstrated significant changes in both pro- and anti-inflammatory pathways probably balancing the chronic inflammation in the pancreas. Our findings also suggested possible involvement of pancreatic stellate cells in disease progression.

Transcriptome analysis identifies putative multi-gene signature distinguishing benign and malignant pancreatic head mass.

BACKGROUND: Most often, the patients with pancreatic diseases are presented with a mass in pancreatic head region and existing methods of diagnosis fail to confirm whether the head mass is malignant or benign. As subsequent management of the disease hugely depends on the correct diagnosis, we wanted to explore possible biomarkers which could distinguish benign and malignant pancreatic head masses. METHODS: In order to address that gap, we performed a case-control study to identify genome-wide differentially expressed coding and noncoding genes between pancreatic tissues collected from benign and malignant head masses. These genes were next shortlisted using stringent criteria followed by selection of top malignancy specific genes. They subsequently got validated by quantitative RT-PCR and also in other patient cohorts. Survival analysis and ROC analysis were also performed. RESULTS: We identified 55 coding and 13 noncoding genes specific for malignant pancreatic head masses. Further shortlisting and validation, however, resulted in 5 coding genes as part of malignancy specific multi-gene signature, which was validated in three independent patient cohorts of 145 normal and 153 PDAC patients. We also found that overexpression of these genes resulted in survival disadvantage in the patients and ROC analysis identified that combination of 5 coding genes had the AUROC of 0.94, making them potential biomarker. CONCLUSIONS: Our study identified a multi-gene signature comprising of 5 coding genes (CDCA7, DLGAP5, FOXM1, TPX2 and OSBPL3) to distinguish malignant head masses from benign ones.

Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2.

BACKGROUND: The world is going through the critical phase of COVID-19 pandemic, caused by human coronavirus, SARS-CoV-2. Worldwide concerted effort to identify viral genomic changes across different sub-types has identified several strong changes in the coding region. However, there have not been many studies focusing on the variations in the 5' and 3' untranslated regions and their consequences. Considering the possible importance of these regions in host mediated regulation of viral RNA genome, we wanted to explore the phenomenon. METHODS: To have an idea of the global changes in 5' and 3'-UTR sequences, we downloaded 8595 complete and high-coverage SARS-CoV-2 genome sequence information from human host in FASTA format from Global Initiative on Sharing All Influenza Data (GISAID) from 15 different geographical regions. Next, we aligned them using Clustal Omega software and investigated the UTR variants. We also looked at the putative host RNA binding protein (RBP) and microRNA binding sites in these regions by 'RBPmap' and 'RNA22 v2' respectively. Expression status of selected RBPs and microRNAs were checked in lungs tissue. RESULTS: We identified 28 unique variants in SARS-CoV-2 UTR region based on a minimum variant percentage cut-off of 0.5. Along with 241C>T change the important 5'-UTR change identified was 187A>G, while 29734G>C, 29742G>A/T and 29774C>T were the most familiar variants of 3'UTR among most of the continents. Furthermore, we found that despite the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs. CONCLUSION: Our results, shows for the first time in SARS-Cov-2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. The knowledge might be helpful in developing anti-viral compounds in future.

High pressure study of magnetocaloric effect in Ho3Co and Tb3Co.

The magnetocaloric effect of intermetallic compounds of Tb3Co and Ho3Co is studied under high pressures up to ∼1 GPa using pressure dependent dc magnetisation and specific heat measurements at ambient conditions. The magnetic entropy change (-ΔS M) obtained from magnetisation data and adiabatic change in temperature (ΔT ad) determined from zero-field specific heat and magnetisation data are found to be nearly identical within error limits with those deduced from purely field dependent specific heat experiments. With increasing hydrostatic pressure to ∼1 GPa, the -ΔS M and ΔT ad, both show a significant enhancement of about 37% and 13%, respectively for 9 T field change in case of Tb3Co. On the other hand, Ho3Co exhibits a decrease of about 8% in both -ΔS M and ΔT ad with increasing pressure. The refrigerant capacity (RC) also increases from 650 J kg-1 to 847 J kg-1 in the case of Tb3Co and it goes down from 665 J kg-1 to 615 J kg-1 for Ho3Co for an increase of pressure to 1 GPa. With increasing pressure, the peak widths of both -ΔS M and ΔT ad increase in case of Tb3Co, although the increase is more in -ΔS M. However, such noticeable changes in peak widths with pressure were not observed in Ho3Co. At ambient pressure, peak of -ΔS M ([Formula: see text]) scales with [Formula: see text] for both the compounds, consistent with the prediction of mean field theory (MFT) for second order magnetic transition. However, deviation from MFT was noticed at high pressures as [Formula: see text] was found to scale with [Formula: see text] instead of [Formula: see text] for both the alloys. Further, normalised -ΔS M curves for different ΔH and pressures collapse on a single universal curve in both the compounds thereby indicating that the second order magnetic transition persists even up to ∼1 GPa pressure.

Comparison of tumour and serum specific microRNA changes dissecting their role in pancreatic ductal adenocarcinoma: a meta-analysis.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is considered as one of the most aggressive cancers lacking efficient early detection biomarkers. Circulating miRNAs are now being considered to have potency to be used as diagnostic and prognostic biomarkers in different diseases as well as cancers. In case of cancer, a fraction of the circulating miRNAs is actually derived from the tumour tissue. This fraction would function as stable biomarker for the disease and also would contribute to the understanding of the disease development. There are not many studies exploring this aspect in pancreatic cancer and even there is not much overlap of results between existing studies. METHODS: In order to address that gap, we performed a miRNA microarray analysis to identify differentially expressed circulating miRNAs between PDAC patients and normal healthy individuals and also found two more similar datasets to perform a meta-analysis using a total of 182 PDAC patients and 170 normal, identifying a set of miRNAs significantly altered in patient serum. Next, we found five datasets studying miRNA expression profile in tumour tissues of PDAC patients as compared to normal pancreas and performed a second meta-analysis using data from a total of 183 pancreatic tumour and 47 normal pancreas to detect significantly deregulated miRNAs in pancreatic carcinoma. Comparison of these two lists and subsequent search for their target genes which were also deregulated in PDAC in inverse direction to miRNAs was done followed by investigation of their role in disease development. RESULTS: We identified 21 miRNAs altered in both pancreatic tumour tissue and serum. While deciphering the functions of their target genes, we characterized key miR-Gene interactions perturbing the biological pathways. We identified important cancer related pathways, pancreas specific pathways, AGE-RAGE signaling, prolactin signaling and insulin resistance signaling pathways among the most affected ones. We also reported the possible involvement of crucial transcription factors in the process. CONCLUSIONS: Our study identified a unique meta-signature of 21 miRNAs capable of explaining pancreatic carcinogenesis and possibly holding the potential to act as biomarker for the disease detection which could be explored further.

High pressure study of magnetic properties of Tb3Co.

The magnetic properties of rare earth rich intermetallic compound, Tb3Co, were studied under external pressures up to ∼1.21 GPa. The application of external pressure results in a decrease of the transition temperatures, [Formula: see text] (paramagnetic to modulated antiferromagnetic) by about 6 K, and the order to order transition that coincides with a glass transition at 72 K by about 15 K, respectively. The low temperature drop in the zero-field cooled magnetisation signifying the strengthening of spin-orbit coupling remains more or less unaffected (shifts only by 3 K) by the external pressures but significant changes in the magnetic behaviour were observed above 40 K. The overall long range non-collinear magnetic order coexisting with glassy behaviour (below 72 K) is sustained even at ∼1.07 GPa pressure. The rate of decay of [Formula: see text] (d[Formula: see text]) is found to be linear with -7.2 K GPa-1 up to ∼0.9 GPa and then it deviates from linearity. The magnetic relaxations and memory effects studied under different measurement protocols confirm the presence of glassiness right up to the highest pressure, although the glassy behaviour is weakened to some extent with increasing pressure as reflected by faster relaxations.

Magnetic glassy behaviour coupled with long range non-collinear magnetic order in Tb3Co.

Detailed and systematic study of rare earth rich intermetallic compound Tb3Co, using dc magnetisation, neutron powder diffraction, and linear and non-linear ac-susceptibilities, shows the presence of an unexpected magnetic glassy state along with complex non-collinear or modulated antiferromagnetic (AFM) order. Our neutron diffraction study shows that the magnetic structure remains more or less the same except for a decrease in moment values in the temperature range of 2 K-70 K and rules out any phase transition around 30 K. However, it reveals sharp changes in structural parameters around 30 K, which indicates strong spin-lattice coupling and change in strength. It appears to be mainly responsible for the observed increase in ZFC magnetisation on warming around 30 K. Another important unexpected result of this study is the strong frequency dispersion in linear and non-linear (higher order harmonics) ac-susceptibilities below [Formula: see text] K. The analysis in terms of various spin glass theoretical formulisms and even stronger frequency dispersion in non-linear susceptibilities provides evidence for the presence of a spin glass like state in Tb3Co. The final picture that emerges out of this study is that a spin glass like state coexists with the long range modulated AFM order below 72 K.

MicroRNA-340-mediated degradation of microphthalmia-associated transcription factor (MITF) mRNA is inhibited by coding region determinant-binding protein (CRD-BP).

Alternative cleavage and polyadenylation generates multiple transcript variants producing mRNA isoforms with different length 3'-UTRs. Alternative cleavage and polyadenylation enables differential post-transcriptional regulation via the availability of different cis-acting elements in 3'-UTRs. Microphthalmia-associated transcription factor (MITF) is a master regulator of melanocyte development and melanogenesis. This central transcription factor is also implicated in melanoma development. Here, we show that melanoma cells favor the expression of MITF mRNA with a shorter 3'-UTR. We also establish that this isoform is regulated by a micro RNA (miRNA/miR), miR-340. miR-340 interacts with two of its target sites on the MITF 3'-UTR, causing mRNA degradation as well as decreased expression and activity of MITF. Conversely, the RNA-binding protein, coding region determinant-binding protein, was shown to be highly expressed in melanoma, directly binds to the 3'-UTR of MITF mRNA, and prevents the binding of miR-340 to its target sites, resulting in the stabilization of MITF transcripts, elevated expression, and transcriptional activity of MITF. This regulatory interplay between RNA-binding protein and miRNA highlights an important mechanism for the regulation of MITF in melanocytes and malignant melanomas.

MicroRNA-340-mediated degradation of microphthalmia-associated transcription factor mRNA is inhibited by the coding region determinant-binding protein.

Alternative cleavage and polyadenylation generate multiple transcript variants of mRNA isoforms with different length of 3'-untranslated region (UTR). Alternative cleavage and polyadenylation enable differential post-transcriptional regulation of transcripts via the availability of different cis-acting elements in 3'-UTRs. Microphthalmia-associated transcription factor (MITF) is a master regulator of melanocyte development and melanogenesis. It has also been implicated in melanoma development. Here we show that melanoma cells favor the expression of MITF mRNA with shorter 3'-UTR. This isoform of mRNA is regulated by microRNA, miR-340. miR-340 interacts with two of its target sites on the 3'-UTR of MITF mRNA, causing mRNA degradation and decreased expression and activity of MITF. On the other hand, the RNA-binding protein coding region determinant-binding protein, shown to be highly expressed in melanoma, directly binds to the 3'-UTR of MITF mRNA and prevents the binding of miR-340 to its target sites, resulting in stabilization of the MITF transcript and elevated expression and transcriptional activity of MITF. This interplay between RNA-binding protein and miRNA describes the important mechanism of regulation of MITF in melanocytes and malignant melanomas.

Wnt signaling stimulates transcriptional outcome of the Hedgehog pathway by stabilizing GLI1 mRNA.

Wnt and Hedgehog signaling pathways play central roles in embryogenesis, stem cell maintenance, and tumorigenesis. However, the mechanisms by which these two pathways interact are not well understood. Here, we identified a novel mechanism by which Wnt signaling pathway stimulates the transcriptional output of Hedgehog signaling. Wnt/beta-catenin signaling induces expression of an RNA-binding protein, CRD-BP, which in turn binds and stabilizes GLI1 mRNA, causing an elevation of GLI1 expression and transcriptional activity. The newly described mode of regulation of GLI1 seems to be important to several functions of Wnt, including survival and proliferation of colorectal cancer cells.

CRD-BP protects the coding region of betaTrCP1 mRNA from miR-183-mediated degradation.

miRNAs are largely known to base pair with the 3'UTR of target mRNAs, downregulating their stability and translation. mRNA of betaTrCP1 ubiquitin ligase is very unstable, but unlike the majority of mRNAs where 3'UTR determines the rate of mRNA turnover, betaTrCP1 mRNA contains cis-acting destabilizing elements within its coding region. Here we show that degradation of mRNA of betaTrCP1 is miRNA dependent and identify miR-183 as a microRNA that interacts with the coding region of betaTrCP1 mRNA. Argonaute2 interacts with the same region of betaTrCP1 mRNA in an miR-183-dependent manner. Inhibition of miR-183 function or disruption of the miR-183-binding site stabilizes betaTrCP1 mRNA and elevates betaTrCP1 levels, resulting in activation of the SCF(betaTrCP) E3 ubiquitin ligase. We previously showed that the RNA-binding protein CRD-BP binds to the coding region of betaTrCP1 mRNA and stabilizes it. Here we demonstrate that CRD-BP prevents degradation of betaTrCP1 mRNA by attenuating its miR-183-dependent interaction with Ago2.

An RNA-binding respiratory component mediates import of type II tRNAs into Leishmania mitochondria.

Transport of tRNAs across the inner mitochondrial membrane of the kinetoplastid protozoon Leishmania requires interactions with specific binding proteins (receptors) in a multi-subunit complex. The allosteric model of import regulation proposes cooperative and antagonistic interactions between two or more receptors with binding specificities for distinct tRNA families (types I and II, respectively). To identify the type II receptor, the gene encoding RIC8A, a subunit of the complex, was cloned. The C-terminal region of RIC8A is homologous to subunit 6b of ubiquinol cytochrome c reductase (respiratory complex III), while the N-terminal region has intrinsic affinity for type II, but not for type I, tRNAs. RIC8A is shared by the import complex and complex III, indicating its bi-functionality, but is assembled differently in the two complexes. Knockdown of RIC8A in Leishmania lowered the mitochondrial content of type II tRNAs but raised that of type I tRNAs, with downstream effects on mitochondrial translation and respiration, and cell death. In RIC8A knockdown cells, a subcomplex was formed that interacted with type I tRNA, but the negative regulation by type II tRNA was lost. Mitochondrial extracts from these cells were defective for type II, but not type I, import; import and regulation were restored by purified RIC8A. These results provide evidence for the relevance of allosteric regulation in vivo and indicate that acquisition of new tRNA-binding domains by ancient respiratory components have played a key role in the evolution of mitochondrial tRNA import.

The alpha-subunit of Leishmania F1 ATP synthase hydrolyzes ATP in presence of tRNA.

Import of tRNAs into the mitochondria of the kinetoplastid protozoon Leishmania requires the tRNA-dependent hydrolysis of ATP leading to the generation of membrane potential through the pumping of protons. Subunit RIC1 of the inner membrane RNA import complex is a bi-functional protein that is identical to the alpha-subunit of F1F0 ATP synthase and specifically binds to a subset (Type I) of importable tRNAs. We show that recombinant, purified RIC1 is a Type I tRNA-dependent ATP hydrolase. The activity was insensitive to oligomycin, sensitive to mutations within the import signal of the tRNA, and required the cooperative interaction between the ATP-binding and C-terminal domains of RIC1. The ATPase activity of the intact complex was inhibited by anti-RIC1 antibody, while knockdown of RIC1 in Leishmania tropica resulted in deficiency of the tRNA-dependent ATPase activity of the mitochondrial inner membrane. Moreover, RIC1 knockdown extracts failed to generate a membrane potential across reconstituted proteoliposomes, as shown by a rhodamine 123 uptake assay, but activity was restored by adding back purified RIC1. These observations identify RIC1 as a novel form of the F1 ATP synthase alpha-subunit that acts as the major energy transducer for tRNA import.