Unassigned MURF1 of kinetoplastids codes for NADH dehydrogenase subunit 2
© Kannan and Burger; licensee BioMed Central Ltd. 2008
Received: 15 November 2007
Accepted: 02 October 2008
Published: 02 October 2008
In a previous study, we conducted a large-scale similarity-free function prediction of mitochondrion-encoded hypothetical proteins, by which the hypothetical gene murf1 (maxicircle unidentified reading frame 1) was assigned as nad2, encoding subunit 2 of NADH dehydrogenase (Complex I of the respiratory chain). This hypothetical gene occurs in the mitochondrial genome of kinetoplastids, a group of unicellular eukaryotes including the causative agents of African sleeping sickness and leishmaniasis. In the present study, we test this assignment by using bioinformatics methods that are highly sensitive in identifying remote homologs and confront the prediction with available biological knowledge.
Comparison of MURF1 profile Hidden Markov Model (HMM) against function-known profile HMMs in Pfam, Panther and TIGR shows that MURF1 is a Complex I protein, but without specifying the exact subunit. Therefore, we constructed profile HMMs for each individual subunit, using all available sequences clustered at various identity thresholds. HMM-HMM comparison of these individual NADH subunits against MURF1 clearly identifies this hypothetical protein as NAD2. Further, we collected the relevant experimental information about kinetoplastids, which provides additional evidence in support of this prediction.
Our in silico analyses provide convincing evidence for MURF1 being a highly divergent member of NAD2.
The single-celled flagellated eukaryotes of the group kinetoplastids include notorious human pathogens such as Trypanosoma and Leishmania. Mitochondrial (mt) genomes of numerous trypanosomatids have been sequenced, with complete and nearly complete mtDNA sequences available for five species: Leishmania tarentolae (GenBank Accession No: NC_000894), Trypanosoma brucei (M94286), T. cruzi (DQ343645), Crithidia oncopelti (X56015), Leptomonas seymouri (DQ239758), and major portions of mtDNA for two other members of the group: Leishmania major (AH015294), Leptomonas collosoma (AH015822). For a review, see .
The unassigned open reading frame (ORF) murf1 in T. brucei mtDNA has been known for 25 years, but until today, there is no protein of known function that shares significant sequence similarity with this ORF . In a recent study, we conducted a comprehensive function prediction of all hypothetical mitochondrion-encoded proteins using a machine-learning-based classifier MOPS . This classifier does not rely on sequence similarity but rather on a host of other features including physico-chemical properties of proteins, and hence should be able to detect remote homologs. MOPS predicted, but only with moderate support, MURF1 of the kinetoplastid Phytomonas serpens as subunit 2 (NAD2) of the NADH-Ubiquinone Oxidoreductase (NADHdh) or Complex I of the electron transport chain – a multi-complex pathway embedded in the inner mitochondrial membrane. NADHdh is the largest complex of this pathway with ~45 distinct subunits, seven of which are usually encoded in the mitochondria. We chose to scrutinize this function assignment in detail, motivated by several reasons: the long-standing controversy surrounding MURF1, the large available body of related biological knowledge, and the significance of this organismal group for human health [2, 4–6].
As mentioned in the Background, the hypothetical protein MURF1 was predicted by the automated similarity-free classifier MOPS to be a divergent NADHdh subunit 2 (NAD2). To test this prediction, we conducted the following analyses.
Sequence – Sequence Comparison
List of FASTA hits for P. serpens MURF1 searched against UniProt
Putative membrane protein
Trypanosoma brucei brucei
NADH dehydrogenase I chain L
Profile – Sequence Comparison
For the identification of distantly related sequences, methods that exploit profiles (i.e., position-specific descriptions of the consensus of a multiple sequence alignment) are more sensitive than those based on pairwise alignment such as BLAST and FASTA. Here, we used PSI-BLAST to generate a MURF1 profile and searched it against NRDB, but no other proteins beyond kinetoplastid MURF1 sequences were found.
Profile HMM – Profile HMM Comparison
Our hypothesis is that MURF1 is a highly derived distant homolog of NAD2. We used Profile HMM – Profile HMM comparison because it is the most sensitive method in identifying distant homologs. In contrast to simple sequence profiles, Profile Hidden Markov Models (HMMs) contain extra information about insertions/deletions and gap scores. HHsearch (the first implementation of this approach), was shown to outperform profile – sequence comparison methods such as PSI-BLAST and HMMER, profile – profile comparison tools such as PROF_SIM and COMPASS and the other HMM – HMM comparison tool PRC .
Best informative hits for the MURF1 profile HMM when searched against profile HMMs from various databases
Best informative hit
NADH-Ubiquinone/plastoquinone (Complex I), various subunits
NADH:Ubiquinone oxidoreductase subunit 2
NDH_I_N Proton-translocating NADH-Quinone oxidoreductase
Best hits for the MURF1 profile HMM when searched against the profile HMMs of all NADH dehydrogenase subunits using HHsearch. The hits are ranked based on E-valuesa
While sequence – sequence comparison and profile HMM – profile HMM comparison point to MURF1 being a subunit of NADHdh, profile – profile comparison against the profile HMMs of individual subunits of NADHdh is able to clearly assign MURF1 to NAD2. In the following, we will confront this in silico prediction with the available biological knowledge. If the MURF1 protein of trypanosomes is indeed NAD2, then the following criteria must apply.
1. There should be no previously annotated nad 2 gene in either mitochondrial or nuclear genomes of kinetoplastids. A nad 2 gene has not been reported in any mitochondrial genome of kinetoplastids. Recently, the sequence of the nuclear genome became available for the P. serpens . Neither genome nor EST data (2,190 ESTs) indicate the presence of this gene.
2. There should be numerous precedents for nad 2 being encoded by mtDNA. The nad 2 gene is mtDNA-encoded by the large majority of eukaryotes (see GOBASE, 'Gene Distribution' http://gobase.bcm.umontreal.ca/searches/compilations.php). The rare species that lack this mitochondrial gene also lack other NADH subunits (Apicomplexa, yeast).
3. The murf1 gene should be transcribed. Evidence for murf1 being expressed rather than being a spurious ORF is provided by several observations. First, the deduced amino acid sequence is conserved across trypanosomes, despite considerable divergence at the nucleotide level. Second, transcription of this gene has been demonstrated in P. serpens .
Notably, a functional NADHdh is crucial to the survival of trypanosomes. Under aerobic conditions (procyclic, insect stage), NADHdh is required as a component of the respiratory chain, to catalyze electron transport toward complex IV. The thus generated proton gradient is utilized for ATP synthesis. Under anaerobic conditions (bloodstream form), a functional NADHdh is equally essential. In the blood stream of mammals, NADHdh provides electrons for the alternative oxidase, a pathway required for maintaining the balance of NADH/NAD+ in the cell. This confirms that trypanosomes depend on a functional NADHdh. In fact, Atovaquone, an anti-leishmanial drug, inhibits the NADHdh activity in P. serpens and this inhibition was suggested to underlie the anti-leishmanial activity of that drug . In this context, the identification of MURF1 as a divergent NAD2 could offer new avenues to the prevention or treatment of trypanosomatid-caused diseases.
List of kinetoplastid MURF1 sequences with GenBank Accession Numbers
Assignment of MURF1
For the function assignment of MURF1, we chose to use sequence-sequence, sequence-profile and profile-profile methods described below, which are most sensitive methods to detect remote homologs.
Sequence – Sequence Comparison
A BLAST (blastp) search was conducted for the MURF1 protein sequence against NCBI's NRDB (non-redundant protein database) (October, 2006; 4,565,699 sequences), with default parameters . In addition, a FASTA search was conducted for the MURF 1 protein sequence against UniProt (release 10.4) with default parameters, at the EBI website http://www.ebi.ac.uk/fasta33.
Profile – Sequence Comparison
This comparison was conducted in two different ways. First, PSI-BLAST was employed to search MURF1 remotely against NCBI's NRDB, with four iterations . Second, we performed profile HMM – sequence comparison using profiles from Pfam version 21.0, executed at the Pfam website http://www.sanger.ac.uk/Software/Pfam.
Profile HMM – Profile HMM Comparison
For Profile HMM – profile HMM comparison, we used HHsearch of the HHpred package, which takes the MURF1 sequence as input and searches against NRDB using PSI-BLAST . The MURF1 homologs obtained from the PSI-BLAST search are then used to generate a profile HMM. As a next step, this MURF1 profile HMM is searched against all profile HMMs of function-known proteins available from the public databases Pfam, PANTHER, SMART, COG, PDB and SCOP.
In addition, we generated our own profile HMMs for each of the 12 NADHdh subunits (1–11 and 4L) from all known sequences of these protein classes. These sequences were clustered at eight different identity thresholds (40, 45, 50, 55, 60, 65, 70 and 75%) using CD-HIT, followed by multiple sequence alignment performed with MUSCLE [16, 17]. (Note: The number of instances for subunit NAD8 and NAD10 are less than 3 at identity thresholds 65 and 75% respectively and hence profile HMMs were not generated below these thresholds for these two subunits) [see Additional file 1]. The multiple alignment served as input for generating profiles using hmmbuild of HMMER version 2.3.2, 2003 package . In order to verify whether profile HMM-profile HMM comparison is efficient in distinguishing the subunits, we tested this approach on the function-known sequences. Herefore, we used NAD2 and NAD5 subunits – the most difficult subunits to distinguish. For evaluating NAD2-profile HMMs, all NAD2 sequences were divided randomly into ten non-overlapping subsets of equal size. A test-profile HMM was generated using one of the subsets, while the remaining nine subsets were used for generating a "master" profile HMM. The NAD2 test-profile HMM was then searched against the NAD2 "master" profile HMM and the NAD5 profile HMM (generated using all NAD5 sequences) using HHsearch. This procedure is repeated ten times. The same test was done for NAD5. All test-profile HMMs were correctly identified at 100%. Finally, the MURF1 profile HMM was searched against all the 84 profiles using HHsearch with default parameters.
We thank Yaoqing Shen for critically reading the manuscript. SK is Canadian Institute for Health Research (CIHR) Strategic Training Fellow in Bioinformatics (Genetics Institute grant STG-63292). This work was supported by grants from the CIHR Genetics Institute (grants MOP-15331 and MOP-79303). The Canadian Institute for Advanced Research (CIAR) is acknowledged for travel and interaction support provided to GB.
- Feagin J: Mitochondrial genome diversity in parasites. Int J Parasitol. 2000, 30 (4): 371-390.PubMed
- Eperon IC, Janssen JWG, Hoeijmakers JHJ, Borst P: The major transcripts of the kinetoplast DNA of Trypanosoma brucei are very small ribosomal RNAs. Nucl Acids Res. 1983, 11 (1): 105-125.PubMedPubMed Central
- Kannan S, Hauth AM, Burger G: Function prediction of hypothetical proteins without sequence similarity to proteins of known function. Protein and Peptide Letters.
- Pappas GJ, Benabdellah K, Zingales B, González A: Expressed sequence tags from the plant trypanosomatid Phytomonas serpens. Mol Biochem Parasitol. 2005, 142 (2): 149-157.PubMed
- Maslov D, Nawathean P, Scheel J: Partial kinetoplast-mitochondrial gene organization and expression in the respiratory deficient plant trypanosomatid Phytomonas serpens. Mol Biochem Parasitol. 1999, 99 (2): 207-221.PubMed
- González-Halphen D, Maslov D: NADH-ubiquinone oxidoreductase activity in the kinetoplasts of the plant trypanosomatid Phytomonas serpens. Parasitol Res. 2004, 92 (4): 341-346.PubMed
- Soding J: Protein homology detection by HMM-HMM comparison. Bioinformatics. 2005, 21 (7): 951-960.PubMed
- Fang J, Wang Y, Beattie DS: Isolation and characterization of complex I, rotenone-sensitive NADH: ubiquinone oxidoreductase, from the procyclic forms of Trypanosoma brucei. Eur J Biochem. 2001, 268 (10): 3075-3082.PubMed
- O'Brien EA, Zhang Y, Yang L, Wang E, Marie V, Lang BF, Burger G: GOBASE – a database of organelle and bacterial genome information. Nucleic Acids Res. 2006, D697-699. 34 Database
- Ostell J: The Entrez search and retrieval system. The NCBI Handbook. 2002
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215 (3): 403-410.PubMed
- Pearson WR: Rapid and sensitive sequence comparison with FASTP and FASTA. Meth Enzymol. 1990, 183: 63-98.PubMed
- Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25 (17): 3389-3402.PubMedPubMed Central
- Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A: Pfam: clans, web tools and services. Nucleic Acids Res. 2006, D247-251. 34 Database
- Soding J, Biegert A, Lupas AN: The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005, W244-248. 33 Web Server
- Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006, 22 (13): 1658-1659.PubMed
- Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res. 2004, 32 (5): 1792-1797.PubMedPubMed Central
- Eddy SR: Profile hidden Markov models. Bioinformatics. 1998, 14 (9): 755-763.PubMed
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