Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies
© Walker and Roberts; licensee BioMed Central Ltd. 2009
Received: 17 September 2008
Accepted: 24 April 2009
Published: 24 April 2009
The Type I interferons (IFN) have major roles in the innate immune response to viruses, a function that is believed to have led to expansion in the number and complexity of their genes, although these genes have remained confined to single chromosomal region in all mammals so far examined. IFNB and IFNE define the limits of the locus, with all other Type I IFN genes except IFNK distributed between these boundaries, strongly suggesting that the locus has broadened as IFN genes duplicated and then evolved into a series of distinct families.
The Type I IFN locus in Bos taurus has undergone significant rearrangement and expansion compared to mouse and human, however, with the constituent genes separated into two sub-loci separated by >700 kb. The IFNW family is greatly expanded, comprising 24 potentially functional genes and at least 8 pseudogenes. The IFNB (n = 6), represented in human and mouse by one copy, are also present as multiple copies in Bos taurus. The IFNT, which encode a non-virally inducible, ruminant-specific IFN secreted by the pre-implantation conceptus, are represented by three genes and two pseudogenes. The latter have sequences intermediate between IFNT and IFNW. A new Type I IFN family (IFNX) of four members, one of which is a pseudogene, appears to have diverged from the IFNA lineage at least 83 million years ago, but is absent in all other sequenced genomes with the possible exception of the horse, a non-ruminant herbivore.
In summary, we have provided the first comprehensive annotation of the Type I IFN locus in Bos taurus, thereby providing an insight into the functional evolution of the Type I IFN in ruminants. The diversity and global spread of the ruminant species may have required an expansion of the Type I IFN locus and its constituent genes to provide broad anti-viral protection required for foraging and foregut fermentation.
Viruses are constantly evolving to find more effective means to survive and multiply in their host species [1–3]. The immune defense system, in turn, exists in a perpetual state of co-evolution with the pathogens to limit infectious disease, a circumstance often likened to an "arms race." The primary defense mechanism against viruses in vertebrates is Type I IFN (interferon) of the innate immune system . It can reasonably be argued that complex organisms like mammals can only survive as long as immune defenses can adjust to the strategies of invading pathogens. Accordingly, a rapidly evolving, adaptable IFN system is essential to mammals if they are to endure viral infections. Type I IFN are also pleiotropic cytokines, with significant roles in modulating adaptive immunity, cell proliferation and cell death, and numerous other processes vital to mammalian health and survival . Most likely as a response to these challenges, Type I IFN demonstrate a complex evolutionary history that has resulted in the divergence of at least eight distinct subfamilies: IFN-kappa (IFNK), IFN-beta (IFNB), IFN-epsilon (IFNE), IFN-delta (IFND), IFN-zeta (IFNZ), IFN-alpha (IFNA), IFN-omega (IFNW), and IFN-tau (IFNT) .
Mammalian Type I IFN probably emerged during tetrapod evolution from an older cytokine family, Type III IFN, which provides the primary viral defense mechanism in fish [6, 7]. It is difficult to determine exactly when Type I and Type III IFN diverged because no Type I IFN has been identified in amphibians, but the split definitely occurred prior to the divergence of birds and mammals approximately 310 million years ago (MYA) [5, 8]. Type III IFN, known more commonly in mammals as either IFN-lambda (IFNL) or interleukin (IL)28 and IL29, is encoded by a five exon gene, opposed to the single exon Type I IFN, and acts through a different receptor complex than Type I IFN [9, 10]. Despite these differences, both Type I and Type III IFN have similar mechanisms of induction, activate the same signaling pathways, and trigger the same biological actions in the target cell . Type III IFN has been retained in some mammalian species including humans and mice but has been lost in others . Even when present, it appears to have assumed a less dominant role as an antiviral agent  and may have been supplanted as major player in antiviral defense with the emergence of contemporary Type I IFN.
All Type I IFN elicit an antiviral response, but some may play a more dominant role as first responders than others. IFNA and IFNB were the first Type I IFN to be characterized in human and have been assumed to constitute and the primary viral defense mechanism [13, 14]. IFNA is released by almost all cell types and a few of its family members, specifically human IFNA2a and IFN2b, are currently approved for treatment of a range of viral diseases including hepatitis B and C, condylomata acuminate (genital warts), and AIDS-related Kaposi sarcoma . IFNB is the main IFN secreted by fibroblasts in response to a viral challenge, but is clearly produced by multiple cell types . It acts in the immediate antiviral response and helps regulate the later expression of several IFNA . IFNW and IFNZ both appear to have developed specific niches in antiviral protection for certain species. IFNW has been implicated in protection against specific viruses, such as parvovirus, particularly in cats [18, 19], while murine IFNZ provides a unique combination of high antiviral activity with relatively low lymphomyeolosuppresive activity , suggesting it may act to suppress viruses targeting the bone marrow and spleen. IFNK is predominately expressed in keratinocytes where it is acts through a unique cell-associated viral protection mechanism [21, 22]. IFNE is expressed in a variety of cell types, but has been suggested on the basis of rather meager evidence to serve a specific role in reproductive tissues either in viral protection or early placental development [5, 23]. IFND and IFNT, on the other hand, are not induced by viruses but instead are released by the early pre-implantation embryos of swine and ruminant species, respectively, where they appear to trigger responses in maternal uterine endometrium that allow the pregnancy to become established [24, 25].
The arrangement of Type I IFN genes within the locus likely reflects the origins and subsequent evolution of individual family members. All Type I IFN in human and mouse are clustered in an approximately 400 kb length of DNA, located on the short arm of chromosome 9 (9p21) in human and on the centromere-proximal region of chromosome 4 (4C4) in mouse [26–28]. Two genes of ancient origin, IFNB and IFNE, define the outer limits of the locus. All the other Type I IFN genes, except IFNK, are distributed between these two ancient genes, indicating the locus has expanded internally as IFN genes duplicated and then evolved into their respective families . However, species-specific expansion and contraction of families has occurred, with some IFN families only existing in certain taxonomic groups. For example, IFND has only been identified in the pig and is absent in the mouse and human, while IFNZ is represented in the mouse, but only remnants of the gene has been found in rats, while it is completely absent in humans [20, 25, 29]. The IFNW, which are considered to have arisen from the IFNA at least 129 MYA [16, 30], constitute a particularly variable grouping. A single functional IFNW and at least two pseudogenes are present in humans, but only a single pseudogene can be identified in mice . Even more bewildering, the family appears to have expanded in cats, which, on the basis of cDNA evidence, possess at least 10 variants , but not even a relic of the open reading frame can be found in the related carnivore, the dog . Ruminant species, such as cattle, are known to possess several, apparently functional, IFNW [33, 34]. There is also one example of a Type I family, the IFNT, that arose relatively recently (36 MYA) in the lineage to the ruminant artiodactyls. As a consequence, the IFNT are absent from all species except those in the sub-order Ruminantia [33, 35]. Together, these data suggest that novel IFN genes can be gained and existing genes discarded in response to specific environmental challenges, which most likely include threats from emerging new pathogens. In addition, existing IFN may become co-opted into new roles unrelated to viral pathogenesis, as has occurred in the case of the IFND [20, 25, 29].
Although it has been clear for some time that there are similarities in the organization of the Type I IFN locus of cattle and that of other species [36, 37], it was equally evident that the bovine locus must have some unique features, most notably because of the existence of the IFNT, genes unique to ruminant species whose protein products, although active in antiviral assays, have a primary role as hormones of pregnancy . Cattle also have multiple IFNB while all non-ruminant species so far examined possess only a single copy IFNB . Together these findings suggest either a decreased restriction on duplication of Type I IFN genes in cattle or evolutionary pressure to acquire additional genes. The recent sequencing of the bovine genome has provided the first opportunity for a detailed study of the Type I IFN locus in a ruminant species. Here we provide a detailed description and full annotation of the bovine locus and some inferences about its evolutionary history.
Most of the IFN gene candidates were identified through the National Center for Biotechnology and Information (NCBI)'s bovine genome resource by using the basic local alignment search tools (BLAST) http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9913. Additional searches were performed through NCBI by using the appropriate genome resource http://www.ncbi.nlm.nih.gov/mapview/ for other species, which are discussed later in this section, and by using the basic nucleotide BLAST suite http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome[41, 42]. Several combinations of BLAST algorithms and databases within NCBI were utilized for this work and are described below .
MegaBLAST was designed to compare highly related nucleotide sequences and works best when the target sequence has a 95% identity or higher to the query sequence.
Cross-species megaBLAST, also referred to as discontiguous BLAST, is a derivative of megBLAST that ignores certain bases, thereby allowing mismatches. It was designed to compare nucleotide sequences from one species to nucleotide sequences in another species.
BLASTN also compares nucleotide query sequences to a nucleotide database. This algorithm is slower than megaBLAST, but it can identify shorter sequence matches than megaBLAST. It was not specifically designed for cross-species comparisons.
TBLASTN was designed to compare a protein sequence with a nucleotide database dynamically translated in all reading frames.
The "genome (reference)" database represents the most current publicly available assembly of a genome. The most current assembly of the bovine genome at the time this work was completed was assembly 3.1. The most current assembly for other species examined in this work are placed in parenthesis here – human (36.2), mouse (37.1), horse (1.1), and dog (2.1).
The "WGS contigs" database contains the contigs, or overlapping unassembled sequences, that forms the basis for the assembled genome. Both pig and cat do not have an assembled genome available at this time and only the "WGS contigs" database could be searched for genomic information for these species.
The "traces-WGS" database contains the trace data for whole genome shotgun sequence (WGS) bacterial artificial chromosome (BAC) end sequencing. This database contains single pass sequencing reads that are not trimmed based on quality or vector contamination.
The "nucleotide collection (nr/nt)" database contains all Genbank, RefSeq, EMBL (Europe's primary nucleotide database), DNA Database of Japan (DDJB), and many Protein Databank (PDB) sequences. The "nucleotide (nr/nt)" database is subdivided into "human nucleotide (nr/nt)," "mouse nucleotide (nr/nt)," and "others nucleotide (nr/nt)" databases. The "others nucleotide (nr/nt)" database does not contain any mouse or human sequences.
Query sequences used for the genomic searches.
The Bovine Genome Sequencing and Annotation Consortium created a consensus predicted gene set through an algorithm, termed GLEAN, developed during the annotation of the honey bee that used latent class analysis to automatically combine disparate gene prediction evidence . Since the majority of positive megaBLAST, cross-species megaBLAST, and TBLASTN matches were clustered on two scaffolds, Chr8.25 [Genbank: NW_001495421] and Chr8.34 [Genbank:NW_001495430], all GLEAN models on those two scaffolds were also annotated through Apollo http://apollo.berkeleybop.org/current/index.html[45, 46]. In brief, Apollo is a genome annotation viewer and editor that was originally designed for the annotation of the Drosophila melanogaster genome. The Bovine Genome Sequencing and Annotation Consortium created input files for Apollo containing EST matches, cDNA matches, translated protein matches, and gene model data including all GLEAN models for the bovine genome assembly 3.1. GLEAN models present on scaffolds Chr8.25 and Chr8.34 that had not been identified in the aforementioned searches were queried through BLASTN and discontiguous megaBLAST in the "others nucleotide collection (nr/nt)" and "human nucleotide collection (nr/nt)" databases to verify their status as IFN genes or another gene family. Discontiguous megaBLAST and TBLASTN searches in human, mouse, equine, porcine, feline, and canine "genomic (reference)" and "WGS contigs" databases were performed for the unique IFN family discovered during the annotation of Chr8.34.
The 64 identified IFN genes and pseudogenes and the original query cDNA from Genbank (Table 1) were aligned through CLUSTALW in BioEdit version 7.09 http://www.mbio.ncsu.edu/BioEdit/BioEdit.html[47, 48]. A pairwise comparison to known IFN nucleotide sequences was performed through the Maximum Composite Likelihood method in MEGA version 4 (MEGA4) http://www.megasoftware.net/ to determine the IFN family for each gene [50, 51].
IFNT was queried with megaBLAST in the bovine "traces-WGS" database to validate the number of IFN genes present in the genome. Bovine sequence matches that had greater than 94% sequence identities to the query IFNT for more than 400 basepairs (bp) were visually inspected. An IFNT match was counted as a positive if the sequence had greater than 98% identity to an IFNT cDNA in the portion of the trace with a quality score, available through NCBI, higher than 40 on a scale between 0 and 100. The total number of IFNT matches in the WGS contig database was divided by the bovine genome coverage to approximate the total IFNT gene number.
Alignments for the genomic IFN ORFs were created through ClustalW in BioEdit version 7.09, with individual genes denoted by their GLEAN numbers. Phylogenetic trees were constructed in MEGA4 through the Neighbor-joining (NJ) method with bootstrapping test (1000 replicates). The tree was rooted to IFNK  and a second tree was created with the assumption of a non-uniform rate of change between sites (gamma = 1).
Identification of repetitive elements
The localization and identity of all repetitive elements were determined by using the RepeatMasker program http://www.repeatmasker.org/, which uses the RepBase library of repeat elements . Sub-locus 1, corresponding to 20000–711500 bp in scaffold Chr8.25, and sub-locus 2, corresponding to 2000–446000 bp in scaffold Chr8.34, sequences were first selected through Apollo and imported into a word processing program, Microsoft Word. All gaps within the scaffolds, which are represented by an "N" in the bovine assembly, were removed manually. IFN sub-loci sequences were then analyzed in RepeatMasker version 3.1.9 run in default mode with blastp version 2.0MP-WashU http://blast.wustl.edu/ to determine the percentage of repetitive elements. Bos taurus was set as the assumed species within the program parameters. Simple repeats and low complexity regions were not masked, which means they were not excluded as start sites for a BLAST match, and the matrix was optimized for 42% GC content based on sub-loci optimization pre-runs.
Results and discussion
IFN Gene Families in Bos taurus
Cross-species comparison of IFN subfamilies.
The IFNA and IFNB are also present in multiple copies, with 13 and 6 genes, respectively, although neither family is as large as the IFNW. An apparent IFNB pseudogene, deemed nonfunctional due to a frameshift deletion, also exists.
IFND are only represented as three pseudogenes, a not unexpected finding, as a functional gene has only been reported previously for the pig .
Three apparently functional IFNT are found within the locus. Surprisingly none of these provide an exact match for any of the many cDNA and gene sequences that have previously been reported. Previous mRNA sequencing of the IFNT family had indicated that at least 18 bovine IFNT might exist . Only three IFNT are present in the bovine genome assembly 3.1, however. One particular, well established sub-family, the IFNT2 grouping , is not represented at all in the assembly. Additional analysis revealed 45 acceptable matches to IFNT in the WGS contig database. Since the bovine genome at this time has 7.1 X coverage, the number of IFNT matches divided by this coverage value suggests the possibility of around six IFNT. One explanation is that these "extra" genes have been lost in the assembly process, but even this higher value is still significantly lower than the 10 to 18 IFNT previously believed to exist. Some of the latter are most likely alleles.
Most interestingly, we detected a novel Type I IFN, which, as we shall discuss later, consists of three potentially functional genes and one pseudogene, none of which provides a close sequence match with any previously described Type I IFN. For convenience, and until an appropriate nomenclature is approved, this new family will be termed IFNX.
A weak sequence identity to IFNL was found on chromosome 13, specifically located on scaffold Chr13.80 [Genbank:NW_001493172] from 635,850 to 636,120 bp. This sequence appears not to encode a functional gene in either the 3.1 assembly or the WGS contig database. These data suggest that the Type III IFN family exists only as a relic and is no longer a functional component in bovine pathogen defenses.
There are three clusters of IFNA/IFNW. Two of them are on sub-locus 1, one at the proximal end, the second placed about half way along (Fig. 2). A gene set in the first IFNA/IFNW cluster 1 is a palindrome to one in the second cluster. The corresponding gene pairs have complete nucleotide identity within their coding regions, suggesting that the duplication or gene conversion event that led to their formation occurred quite recently. The third cluster of IFNA/IFNW is at the distal end of sub-locus 2, but lacks the duplicated group of four genes in IFNA/IFNW clusters 1 and 2.
Only one non-IFN gene is detectable within sub-loci 1 and 2, an intronless kelch-like 9 (KLHL9) located 33.5 kb proximal to IFNA/IFNW cluster 2 in sub-locus 1 (Fig. 2). The orthologous KLHL9 gene can be found in the Type I IFN locus of the mouse approximately 25 kb from the nearest functional IFN (IFNA8)  and 29 kb from the nearest IFN (IFNA6) in human. The fact KLHL9 has resisted duplication despite residing close to genes undergoing multiple duplications is noteworthy and possibly indicates that multiple copies of this gene are not well tolerated.
Divergence within IFNA/IFNW clusters.
0.086 ± 0.007
0.071 ± 0.007
0.063 ± 0.006
0.053 ± 0.006
0.04 ± 0.006
0.045 ± 0.006
The IFNT and two IFNW pseudogenes are neighbors at the distal end of sub-locus 1, suggesting that this cluster of genes originated from an IFNW that had become isolated from other IFNW before the divergence of the IFNT. Its unique position outside the IFNA/IFNW clusters and close to the edge of the sub-locus may have permitted the rapid expansion and evolution of the IFNT family without the restraints placed on the clustered IFNW.
All non-ruminant species examined to date, including mouse, human, cats, dogs, rabbits, and pigs, contain only one IFNB . In cattle, this family has clearly expanded and extends from the distal end of IFNA/IFNW cluster 3 to the end of sub-locus 2. Interspersed within these multiple IFNB are members of the previously unidentified IFN family, IFNX. Again, it is tempting to hypothesize that the IFNX and expanded IFNB family were able to emerge due to their location on the edge of the sub-locus 2, as suggested for the IFNT in sub-locus 1.
Repetitive Elements within Sub-loci
Repetitive elements within the bovine Type I IFN sub-loci.
Total interspersed repeats:
Palindromic IFN within IFNA/IFNW clusters 1 and 2
Two different evolutionary processes, either gene duplication or gene conversion, could possibly explain the existence of the IFNA/IFNW palindromic gene sets. Gene duplication involves the formation of a new gene copy. Gene conversion, on the other hand, does not generate new gene copies, but instead homogenizes existing genes. Both gene duplication and gene conversion have been specifically implicated in the evolution of the IFNA in human, chimpanzee, dog, rhesus monkey, rat, and mouse [30, 61, 62]. Gene conversion, specifically, was predicted by two different statistical programs, GARD and GENECONV, in humans, chimpanzee, rhesus monkey, and mice. Furthermore, despite IFNA genes aligning in conserved positions on a locus map for chimpanzees and humans, the subfamily separated into species-specific clades on phylogenetic analysis , strongly indicating gene conversion has occurred in the IFNA subfamily in these two species. Although gene duplications cannot be unambiguously distinguished from gene conversions , the latter seldom involve sequence longer than 1 kb in mammals, with 3 kb considered the maximum length . Therefore, when the sequence tract involved is "too large" for gene conversion, gene duplication is usually implicated . The palindomic gene set involves at least a 27 kb tract, far exceeding this size limit and reducing the likelihood of a conversion event. Therefore, a segmental duplication event, which is a specific type of gene duplication that involves a large segment of a locus, combined with an inversion is the best explanation for the palindrome .
Selective Pressure on the ORF of Type I IFN Subfamilies
Comparison of the rate of non-synonymous nucleotide change relative to the rate of synonymous change can provide information about the type of selection operating on the members of a multigene families . If neutral selection is occurring, then all nucleotides in a sequence are equally likely to change. Consequently the rate of synonymous nucleotide changes (dS) will be equal to the rate of non-synonymous changes (dN) and dS:dN will equal 1. Rapid change in the amino acid sequence is the desired endpoint for positive selective pressure. Hence, in this scenario, dN will exceed dS, and dN:dS will be greater than 1. Conversely, if strong selection against amino acid change is present (purifying selection), dN will be less than dS and dN:dS will be less than 1. Virtually all pairwise comparisons within IFNA, whatever the species [61, 67], and IFNT  have shown the overall value for dN not to be significantly higher than dS. Indeed, dN values have been generally calculated to be lower than dS, consistent with the conclusion that there has not been strong positive selection for amino acid change within the coding regions of these subfamilies of IFN.
Purifying selection within IFNW and IFNA coding regions.
Selection in IFNB.
The classic model of gene duplication states that after a duplication event one gene continues to perform the ancestral function while the second either rapidly evolves to fill a new niche or becomes inactive [65, 68, 69]. As a consequence gene duplication is usually followed by a period in which there is an acquisition of non-synonymous nucleotide changes in one of the two genes, leading to a divergence in amino acid sequence. This temporary relaxation of purifying selection, in which dN:dS approaches 1, permits the gene to become fine-tuned to its new role or, more commonly, results in pseudogenization. Such a sequence of events does not appear to have occurred during the large scale expansion of the IFNW family where there is strong evidence for purifying selection operating on the coding regions of the genes (Fig. 4 & Table 5). One potential explanation is that sub-functionalization is occurring through alterations in the manner in which these genes are subjected to transcriptional control rather than in the structure of the proteins themselves. Evidence for positive selective pressure in the regulatory regions of IFNW would strongly support this hypothesis, but a detailed promoter analysis is beyond the scope of this work.
IFNX: Evidence for a novel subfamily
Previous studies of IFNA have identified three regions that are strongly associated with IFN-receptor interaction and are termed interferon receptor recognition peptides (IRRP)1–3 [70–72]. IRRP1 (27–35) and IRRP2 (78–105) control the initial binding of IFN to the Type I receptor and are highly conserved among IFNA. IRRP3 (123–140) modulates the downstream signaling pathways, so that amino acid changes in this region can explain some differences in biological activity among different IFNA. The protein products of the three IFNX do not possess identical IRRP1 and IRRP2 motifs as IFNA, but these two regions are highly conserved within the subfamily, emphasizing, first, the possible importance of this motif and second that the IFNX family is unique and distinct from IFNA. IRRP3 was absent in GLEAN 24316 again suggesting that it may be a pseudogene. The two remaining IFNX members differed in their IRRP3 sequences, a not unexpected finding as changes in this region may provide subtle differences in biologic activity between the two family members. None of the IFNX genes contain the N-glycosylation sequence (N-X-S/T) common in other Type I IFNs that could alter IFN-receptor interaction.
No evidence for IFNX expression could be found in any EST databases, although, genes with high identity to IFNX exist in the equine genomic database. The conservation of this gene family in species that diverged at least 80 million years ago suggests that the family may have an important function in ungulates. However, the apparent absence of IFNX genes in pigs, also an ungulate, is puzzling. Possibly, IFNX has a specific function in herbivores that is not required in omnivores, most likely in immune defense against particular viruses or other pathogenic organisms affecting such species.
The identification of a novel Type I IFN gene, the IFNX, is an unexpected and possibly important finding. The proteins encoded by this family of genes differ sufficiently in primary sequence from related Type I IFN to justify a separate designation from the related IFNA and IFNB. The presence of a distinct cluster of IFNX within the Type I IFN locus, the phylogenetic position of IFNX as a separate clade within the IFN tree, and the conservation of critical amino acid residues, are totally consistent with classifying the IFNX as a distinct Type I IFN subfamily. Whether IFNX are responsive to a viral challenge and able to interact with the Type I IFN receptor and elicit a typical Type I response in their target cells has yet to be verified. Substantial work will be necessary to characterize this subfamily fully, but its place as a separate clade within the Type I IFN would appear to be assured.
The Type I IFN locus has undergone substantial transformation in ruminants compared to humans and mice. The conserved locus structure has been transformed, subfamilies have expanded, and two subfamilies not present in either humans or mice exist. The division of the locus into two sub-loci may have provided an opportunity for genes to duplicate and contribute to an expanded function of the Type I IFN. The divergence of the successful pecoran ruminant sub-order and its geographic spread might have required improved protection against unique ruminant pathogens. The IFNX sub-family and the greatly expanded ruminant specific IFNW are likely candidates for providing such protection. Radically new functions for Type I IFN might also have been gained, such as the one exemplified by the IFNT, whose appearance coincided with, and possibly permitted, the acquisition of the unique, synepitheliochorial placentation that characterizes the Ruminantia sub-order and requires powerful conceptus signaling before the trophoblast has even attached to the uterine wall . The ancient Type III IFN (IFNL/IL28-29) may have become a casualty of the expansion and broadened the role of the Type I locus, as only an inactive IFNL remains in the bovine genome. It is tempting to speculate that the function of IFNL has been replaced as the component genes of the Type I IFN locus expanded.
The authors concede that the bovine genome assembly is a work in progress and that the predicted arrangement of individual IFN genes may have to be modified as data are reanalyzed. In addition, it is clear that an individual animal possesses unique genomic peculiarities, including inversions, duplications, and presence and absence of specific genes and that the IFN locus of a single Hereford cow may not be replicated precisely in other breeds. Nevertheless, with the exception of the size of the "gap" between the two sub-loci, the organization and sequence of the bovine Type I IFN have remained relatively constant through the most recent assemblies. The unique features of the locus, which include the presence of the gap itself, the arrangements of IFNW/IFNA clusters, the dramatic expansion of the IFNW, the presence of the IFNX, and the separation of IFNT from the IFNW/IFNA clusters are consistent observations and unlikely to undergo drastic re-evaluation in future versions of the assembly.
We would like to thank the Bovine Genome Sequencing and Annotation Consortium for coordinating with this project and providing Apollo training. We would also like to thank Drs. Jonathan Green and Bhanu Telugu for advice on the data analysis (bioinformatics). Funding for this work was provided by NIH grant HD21896.
- Goodbourn S, Didcock L, Randall RE: Interferons: cell signalling, immune modulation, antiviral response and virus countermeasures. J Gen Virol. 2000, 81: 2341-2364.View ArticlePubMedGoogle Scholar
- Iannello A, Debbeche O, Martin E, Attalah LH, Samarani S, Ahmad A: Viral strategies for evading antiviral cellular immune responses of the host. J Leukoc Biol. 2006, 79: 16-35. 10.1189/jlb.0705397.View ArticlePubMedGoogle Scholar
- Randall RE, Goodbourn S: Interferons and viruses: an interplay between induction, signalling, antiviral responses and virus countermeasures. J Gen Virol. 2008, 89: 1-47. 10.1099/vir.0.83391-0.View ArticlePubMedGoogle Scholar
- Stark GR, Kerr IM, Williams BR, Silverman RH, Schreiber RD: How cells respond to interferons. Annu Rev Biochem. 1998, 67: 227-264. 10.1146/annurev.biochem.67.1.227.View ArticlePubMedGoogle Scholar
- Krause CD, Pestka S: Evolution of the Class 2 cytokines and receptors, and discovery of new friends and relatives. Pharmacol Ther. 2005, 106: 299-346. 10.1016/j.pharmthera.2004.12.002.View ArticlePubMedGoogle Scholar
- Levraud JP, Boudinot P, Colin I, Benmansour A, Peyrieras N, Herbomel P, Lutfalla G: Identification of the zebrafish IFN receptor: implications for the origin of the vertebrate IFN system. J Immunol. 2007, 178: 4385-4394.View ArticlePubMedGoogle Scholar
- Lutfalla G, Roest Crollius H, Stange-Thomann N, Jaillon O, Mogensen K, Monneron D: Comparative genomic analysis reveals independent expansion of a lineage-specific gene family in vertebrates: the class II cytokine receptors and their ligands in mammals and fish. BMC Genomics. 2003, 4: 29-10.1186/1471-2164-4-29.PubMed CentralView ArticlePubMedGoogle Scholar
- Hedges SB: The origin and evolution of model organisms. Nat Rev Genet. 2002, 3: 838-849. 10.1038/nrg929.View ArticlePubMedGoogle Scholar
- Uze G, Monneron D: IL-28 and IL-29: newcomers to the interferon family. Biochimie. 2007, 89: 729-734. 10.1016/j.biochi.2007.01.008.View ArticlePubMedGoogle Scholar
- Sheppard P, Kindsvogel W, Xu W, Henderson K, Schlutsmeyer S, Whitmore TE, Kuestner R, Garrigues U, Birks C, Roraback J, et al: IL-28, IL-29 and their class II cytokine receptor IL-28R. Nat Immunol. 2003, 4: 63-68. 10.1038/ni873.View ArticlePubMedGoogle Scholar
- Ank N, Iversen MB, Bartholdy C, Staeheli P, Hartmann R, Jensen UB, Dagnaes-Hansen F, Thomsen AR, Chen Z, Haugen H, et al: An important role for type III interferon (IFN-lambda/IL-28) in TLR-induced antiviral activity. J Immunol. 2008, 180: 2474-2485.View ArticlePubMedGoogle Scholar
- Kotenko SV, Gallagher G, Baurin VV, Lewis-Antes A, Shen M, Shah NK, Langer JA, Sheikh F, Dickensheets H, Donnelly RP: IFN-lambdas mediate antiviral protection through a distinct class II cytokine receptor complex. Nat Immunol. 2003, 4: 69-77. 10.1038/ni875.View ArticlePubMedGoogle Scholar
- Rubinstein M, Rubinstein S, Familletti PC, Miller RS, Waldman AA, Pestka S: Human leukocyte interferon: production, purification to homogeneity, and initial characterization. Proc Natl Acad Sci USA. 1979, 76: 640-644. 10.1073/pnas.76.2.640.PubMed CentralView ArticlePubMedGoogle Scholar
- Stein S, Kenny C, Friesen HJ, Shively J, Del Valle U, Pestka S: NH2-terminal amino acid sequence of human fibroblast interferon. Proc Natl Acad Sci USA. 1980, 77: 5716-5719. 10.1073/pnas.77.10.5716.PubMed CentralView ArticlePubMedGoogle Scholar
- Pestka S: The interferons: 50 years after their discovery, there is much more to learn. J Biol Chem. 2007, 282: 20047-20051. 10.1074/jbc.R700004200.View ArticlePubMedGoogle Scholar
- Pestka S, Krause CD, Walter MR: Interferons, interferon-like cytokines, and their receptors. Immunol Rev. 2004, 202: 8-32. 10.1111/j.0105-2896.2004.00204.x.View ArticlePubMedGoogle Scholar
- Barnes B, Lubyova B, Pitha PM: On the role of IRF in host defense. J Interferon Cytokine Res. 2002, 22: 59-71. 10.1089/107999002753452665.View ArticlePubMedGoogle Scholar
- Paltrinieri S, Crippa A, Comerio T, Angioletti A, Roccabianca P: Evaluation of inflammation and immunity in cats with spontaneous parvovirus infection: consequences of recombinant feline interferon-omega administration. Vet Immunol Immunopathol. 2007, 118: 68-74. 10.1016/j.vetimm.2007.04.007.View ArticlePubMedGoogle Scholar
- de Mari K, Maynard L, Eun HM, Lebreux B: Treatment of canine parvoviral enteritis with interferon-omega in a placebo-controlled field trial. Vet Rec. 2003, 152: 105-108.View ArticlePubMedGoogle Scholar
- Oritani K, Medina KL, Tomiyama Y, Ishikawa J, Okajima Y, Ogawa M, Yokota T, Aoyama K, Takahashi I, Kincade PW, et al: Limitin: An interferon-like cytokine that preferentially influences B-lymphocyte precursors. Nat Med. 2000, 6: 659-666. 10.1038/76233.View ArticlePubMedGoogle Scholar
- Buontempo PJ, Jubin RG, Buontempo CA, Wagner NE, Reyes GR, Baroudy BM: Antiviral activity of transiently expressed IFN-kappa is cell-associated. J Interferon Cytokine Res. 2006, 26: 40-52. 10.1089/jir.2006.26.40.View ArticlePubMedGoogle Scholar
- LaFleur DW, Nardelli B, Tsareva T, Mather D, Feng P, Semenuk M, Taylor K, Buergin M, Chinchilla D, Roshke V, et al: Interferon-kappa, a novel type I interferon expressed in human keratinocytes. J Biol Chem. 2001, 276: 39765-39771. 10.1074/jbc.M102502200.View ArticlePubMedGoogle Scholar
- Matsumiya T, Prescott SM, Stafforini DM: IFN-epsilon mediates TNF-alpha-induced STAT1 phosphorylation and induction of retinoic acid-inducible gene-I in human cervical cancer cells. J Immunol. 2007, 179: 4542-4549.View ArticlePubMedGoogle Scholar
- Roberts RM, Chen Y, Ezashi T, Walker AM: Interferons and the maternal-conceptus dialog in mammals. Semin Cell Dev Biol. 2008, 19: 170-177. 10.1016/j.semcdb.2007.10.007.PubMed CentralView ArticlePubMedGoogle Scholar
- Lefevre F, Guillomot M, D'Andrea S, Battegay S, La Bonnardiere C: Interferon-delta: the first member of a novel type I interferon family. Biochimie. 1998, 80: 779-788. 10.1016/S0300-9084(99)80030-3.View ArticlePubMedGoogle Scholar
- Trent JM, Olson S, Lawn RM: Chromosomal localization of human leukocyte, fibroblast, and immune interferon genes by means of in situ hybridization. Proc Natl Acad Sci USA. 1982, 79: 7809-7813. 10.1073/pnas.79.24.7809.PubMed CentralView ArticlePubMedGoogle Scholar
- Hardy MP, Owczarek CM, Jermiin LS, Ejdeback M, Hertzog PJ: Characterization of the type I interferon locus and identification of novel genes. Genomics. 2004, 84: 331-345. 10.1016/j.ygeno.2004.03.003.View ArticlePubMedGoogle Scholar
- Diaz MO, Pomykala HM, Bohlander SK, Maltepe E, Malik K, Brownstein B, Olopade OI: Structure of the human type-I interferon gene cluster determined from a YAC clone contig. Genomics. 1994, 22: 540-552. 10.1006/geno.1994.1427.View ArticlePubMedGoogle Scholar
- Takahashi I, Kosaka H, Oritani K, Heath WR, Ishikawa J, Okajima Y, Ogawa M, Kawamoto S, Yamada M, Azukizawa H, et al: A new IFN-like cytokine, limitin, modulates the immune response without influencing thymocyte development. J Immunol. 2001, 167: 3156-3163.View ArticlePubMedGoogle Scholar
- Hughes AL: The evolution of the type I interferon gene family in mammals. J Mol Evol. 1995, 41: 539-548. 10.1007/BF00175811.View ArticlePubMedGoogle Scholar
- Yang LM, Xue QH, Sun L, Zhu YP, Liu WJ: Cloning and characterization of a novel feline IFN-omega. J Interferon Cytokine Res. 2007, 27: 119-127. 10.1089/jir.2006.0094.View ArticlePubMedGoogle Scholar
- Roberts RM, Ezashi T, Rosenfeld CS, Ealy AD, Kubisch HM: Evolution of the interferon tau genes and their promoters, and maternal-trophoblast interactions in control of their expression. Reprod Suppl. 2003, 61: 239-251.PubMedGoogle Scholar
- Leaman DW, Roberts RM: Genes for the trophoblast interferons in sheep, goat, and musk ox and distribution of related genes among mammals. J Interferon Res. 1992, 12: 1-11.View ArticlePubMedGoogle Scholar
- Capon DJ, Shepard HM, Goeddel DV: Two distinct families of human and bovine interferon-alpha genes are coordinately expressed and encode functional polypeptides. Mol Cell Biol. 1985, 5: 768-779.PubMed CentralView ArticlePubMedGoogle Scholar
- Roberts RM, Liu L, Guo Q, Leaman D, Bixby J: The evolution of the type I interferons. J Interferon Cytokine Res. 1998, 18: 805-816. 10.1089/jir.1998.18.805.View ArticlePubMedGoogle Scholar
- Iannuzzi L, Gallagher DS, Ryan AM, Di Meo GP, Womack JE: Chromosomal localization of omega and trophoblast interferon genes in cattle and river buffalo by sequential R-banding and fluorescent in situ hybridization. Cytogenet Cell Genet. 1993, 62: 224-227. 10.1159/000133482.View ArticlePubMedGoogle Scholar
- Ryan AM, Gallagher DS, Womack JE: Somatic cell mapping of omega and trophoblast interferon genes to bovine syntenic group U18 and in situ localization to chromosome 8. Cytogenet Cell Genet. 1993, 63: 6-10. 10.1159/000133491.View ArticlePubMedGoogle Scholar
- Roberts RM, Leaman DW, Cross JC: Role of interferons in maternal recognition of pregnancy in ruminants. Proc Soc Exp Biol Med. 1992, 200: 7-18.View ArticlePubMedGoogle Scholar
- NCBI/BLAST Cow Sequences. [http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9913]
- NCBI/Mapviewer Home. [http://www.ncbi.nlm.nih.gov/mapview/]
- Ye J, McGinnis S, Madden TL: BLAST: improvements for better sequence analysis. Nucleic Acids Res. 2006, 34: W6-9. 10.1093/nar/gkl164.PubMed CentralView ArticlePubMedGoogle Scholar
- NCBI/BLAST Home. [http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome]
- McEntyre J, (ed): The NCBI Handbook [Internet]. 2002, Bethesda, MD: The National Library of Medicine (US), National Center for Biotechnology Information
- Elsik CG, Mackey AJ, Reese JT, Milshina NV, Roos DS, Weinstock GM: Creating a honey bee consensus gene set. Genome Biol. 2007, 8: R13-10.1186/gb-2007-8-1-r13.PubMed CentralView ArticlePubMedGoogle Scholar
- Apollo Genome Annotation Curation Tool. [http://apollo.berkeleybop.org/current/index.html]
- Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, et al: Apollo: a sequence annotation editor. Genome Biol. 2002, 3: RESEARCH0082-10.1186/gb-2002-3-12-research0082.PubMed CentralView ArticlePubMedGoogle Scholar
- Biological sequence alignment editor for Win95/98/NT/2K/XP. [http://www.mbio.ncsu.edu/BioEdit/BioEdit.html]
- Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673.PubMed CentralView ArticlePubMedGoogle Scholar
- Molecular Evolutionary Genetics Analysis. [http://www.megasoftware.net]
- Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007, 24: 1596-1599. 10.1093/molbev/msm092.View ArticlePubMedGoogle Scholar
- Tamura K, Nei M, Kumar S: Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA. 2004, 101: 11030-11035. 10.1073/pnas.0404206101.PubMed CentralView ArticlePubMedGoogle Scholar
- RepeatMasker. [http://www.repeatmasker.org/]
- Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J: Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005, 110: 462-467. 10.1159/000084979.View ArticlePubMedGoogle Scholar
- Washington University in St. Louis WU-Blast. [http://blast.wustl.edu/]
- Oritani K, Kincade PW, Zhang C, Tomiyama Y, Matsuzawa Y: Type I interferons and limitin: a comparison of structures, receptors, and functions. Cytokine Growth Factor Rev. 2001, 12: 337-348. 10.1016/S1359-6101(01)00009-0.View ArticlePubMedGoogle Scholar
- Lefevre F, Boulay V: A novel and atypical type one interferon gene expressed by trophoblast during early pregnancy. J Biol Chem. 1993, 268: 19760-19768.PubMedGoogle Scholar
- Ealy AD, Larson SF, Liu L, Alexenko AP, Winkelman GL, Kubisch HM, Bixby JA, Roberts RM: Polymorphic forms of expressed bovine interferon-tau genes: relative transcript abundance during early placental development, promoter sequences of genes and biological activity of protein products. Endocrinology. 2001, 142: 2906-2915. 10.1210/en.142.7.2906.PubMedGoogle Scholar
- Yang S, Arguello JR, Li X, Ding Y, Zhou Q, Chen Y, Zhang Y, Zhao R, Brunet F, Peng L, et al: Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila. PLoS Genet. 2008, 4: e3-10.1371/journal.pgen.0040003.PubMed CentralView ArticlePubMedGoogle Scholar
- Fiston-Lavier AS, Anxolabehere D, Quesneville H: A model of segmental duplication formation in Drosophila melanogaster. Genome Res. 2007, 17: 1458-1470. 10.1101/gr.6208307.PubMed CentralView ArticlePubMedGoogle Scholar
- Apostolou E, Thanos D: Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression. Cell. 2008, 134: 85-96. 10.1016/j.cell.2008.05.052.View ArticlePubMedGoogle Scholar
- Woelk CH, Frost SD, Richman DD, Higley PE, Kosakovsky Pond SL: Evolution of the interferon alpha gene family in eutherian mammals. Gene. 2007, 397: 38-50. 10.1016/j.gene.2007.03.018.PubMed CentralView ArticlePubMedGoogle Scholar
- Miyata T, Hayashida H, Kikuno R, Toh H, Kawade Y: Evolution of interferon genes. Interferon. 1985, 6: 1-30.PubMedGoogle Scholar
- Chen JM, Cooper DN, Chuzhanova N, Ferec C, Patrinos GP: Gene conversion: mechanisms, evolution and human disease. Nat Rev Genet. 2007, 8: 762-775. 10.1038/nrg2193.View ArticlePubMedGoogle Scholar
- Blanco P, Shlumukova M, Sargent CA, Jobling MA, Affara N, Hurles ME: Divergent outcomes of intrachromosomal recombination on the human Y chromosome: male infertility and recurrent polymorphism. J Med Genet. 2000, 37: 752-758. 10.1136/jmg.37.10.752.PubMed CentralView ArticlePubMedGoogle Scholar
- Hurles M: Gene duplication: the genomic trade in spare parts. PLoS Biol. 2004, 2: E206-10.1371/journal.pbio.0020206.PubMed CentralView ArticlePubMedGoogle Scholar
- Hughes AL: The evolution of functionally novel proteins after gene duplication. Proc Biol Sci. 1994, 256: 119-124. 10.1098/rspb.1994.0058.View ArticlePubMedGoogle Scholar
- Cheng G, Chen W, Li Z, Yan W, Zhao X, Xie J, Liu M, Zhang H, Zhong Y, Zheng Z: Characterization of the porcine alpha interferon multigene family. Gene. 2006, 382: 28-38. 10.1016/j.gene.2006.06.013.View ArticlePubMedGoogle Scholar
- Walsh JB: How often do duplicated genes evolve new functions?. Genetics. 1995, 139: 421-428.PubMed CentralPubMedGoogle Scholar
- Ohno S: Evolution by gene duplication. 1970, New York, New York: Springer-Verlag, 1View ArticleGoogle Scholar
- Kumaran J, Wei L, Kotra LP, Fish EN: A structural basis for interferon-alpha-receptor interactions. FASEB J. 2007, 21: 3288-3296. 10.1096/fj.07-8585com.View ArticlePubMedGoogle Scholar
- Piehler J, Schreiber G: Biophysical analysis of the interaction of human ifnar2 expressed in E. coli with IFNalpha2. J Mol Biol. 1999, 289: 57-67. 10.1006/jmbi.1999.2726.View ArticlePubMedGoogle Scholar
- Chill JH, Nivasch R, Levy R, Albeck S, Schreiber G, Anglister J: The human interferon receptor: NMR-based modeling, mapping of the IFN-alpha 2 binding site, and observed ligand-induced tightening. Biochemistry. 2002, 41: 3575-3585. 10.1021/bi011778f.View ArticlePubMedGoogle Scholar
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