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Exploring the mialome of ticks: an annotated catalogue of midgut transcripts from the hard tick, Dermacentor variabilis (Acari: Ixodidae)

Background Ticks are obligate blood feeders. The midgut is the first major region of the body where blood and microbes ingested with the blood meal come in contact with the tick's internal tissues. Little is known about protein expression in the digestive tract of ticks. In this study, for analysis of global gene expression during tick attachment and feeding, we generated and sequenced 1,679 random transcripts (ESTs) from cDNA libraries from the midguts of female ticks at varying stages of feeding. Results Sequence analysis of the 1,679 ESTs resulted in the identification of 835 distinct transcripts, from these, a total of 82 transcripts were identified as proteins putatively directly involved in blood meal digestion, including enzymes involved in oxidative stress reduction/antimicrobial activity/detoxification, peptidase inhibitors, protein digestion (cysteine-, aspartic-, serine-, and metallo-peptidases), cell, protein and lipid binding including mucins and iron/heme metabolism and transport. A lectin-like protein with a high match to lectins in other tick species, allergen-like proteins and surface antigens important in pathogen recognition and/or antimicrobial activity were also found. Furthermore, midguts collected from the 6-day-fed ticks expressed twice as many transcripts involved in bloodmeal processing as midguts from unfed/2-day-fed ticks. Conclusion This tissue-specific transcriptome analysis provides an opportunity to examine the global expression of transcripts in the tick midgut and to compare the gut response to host attachment versus blood feeding and digestion. In contrast to those in salivary glands of other Ixodid ticks, most proteins in the D. variabilis midgut cDNA library were intracellular. Of the total ESTs associated with a function, an unusually large number of transcripts were associated with peptidases, cell, lipid and protein binding, and oxidative stress or detoxification. Presumably, this is consistent with their role in intracellular processing of the blood meal and response to microbial infections. The presence of many proteins with similar functions is consistent with the hypothesis that gene duplication contributed to the successful adaptation of ticks to hematophagy. Furthermore, these transcripts may be useful to scientists investigating the role of the tick midgut in blood-meal digestion, antimicrobial activity or the transmission of tick-borne pathogens.


Background
Ticks are notorious as vectors of a large variety of infectious disease agents such as those that cause Lyme disease, Rocky Mountain spotted fever, human (and animal) anaplasmosis, babesiosis and many others. As obligate hematophagic parasites, tick-borne infectious agents are acquired during the blood-feeding process. The tick midgut is the first tissue that pathogens encounter where infection must be established before they can migrate into the internal body organs and tissues. The effects of digestive enzymes expressed in response to the nutritive elements, especially hemoglobin, and the products of their digestive activities have been shown to inhibit or kill some invading microbes [1][2][3]. However, whether such peptidic fragments would also kill pathogenic microbes is unknown. In addition, antimicrobial peptides defensin and lysozyme have been reported from the midgut of a soft tick [4,5] and evidence of their expression (but not the peptides) was found in the hard tick Dermacentor variabilis. Although few in number, these reports suggest that the tick midgut presents a hostile environment for invading microorganisms. Nevertheless, many survive and succeed in colonising this tissue and penetrating the tick internal organs.
In blood-feeding insects, molecules expressed in the midgut of these disease-transmitting vectors are believed to play an important role in determining initial parasite infection and subsequent development. In tsetse flies, for example, 17 midgut proteins were upregulated and 9 were downregulated in response to blood-meal intake [6]. In mosquitoes, blood feeding induces expression of midgut peptidases such as trypsin, chymotrypsin, aminopeptidase, and carboxypeptidase; enzymes that may contribute to success in Plasmodium infection [7,8]. Changes in midgut transcript expression after a blood meal were also recently reported from the midgut of the sand fly Phlebotomus papatasi [9].
Knowledge of the tick digestive process is even more limited. The primary nutritive element, hemoglobin, is digested intracellularly in acidic phagolysosomes of the digestion cells. Most of the heme is shuttled to these specialised organelles, designated as hemosomes, where this highly reactive species is detoxified to hematin [10,11], a non-crystalline heme aggregate similar (but not identical) to malarial hemozoin [12]. Acid phosphatase and nonspecific esterases have been reported to occur in the midgut of several hard-tick species [13,14] but their molecular structure was not identified. More recently, a cysteine peptidase was identified in the midguts of cattle ticks, Rhipicephalus (Boophilus) microplus [15], while serine peptidases were identified in the midguts of two other tick species, Rhipicephalus appendiculatus [16] and Haemaphysa-lis longicornis [17]. Aside from these few reports, little else is known.
In view of the importance of the midgut proteins in understanding the process of blood-meal digestion as well as the fate of microbial infections, we constructed a midgut cDNA library from blood-fed females of the American dog tick, D. variabilis. We obtained and analysed 1,679 high-quality sequenced random clones from the PCRbased cDNA library which generated 835 unique transcripts. Putative functional assignments were made using BLAST homologies to other proteins in the National Center for Biotechnology Information (NCBI) nonredundant database (NR) and by comparison with a specialised database containing all Acari protein sequences (ACARI) and the EuKaryotic Orthologous Groups (KOG), Protein families and domains (Pfam) and Self-Monitoring, Analysis, and Reporting Technology (SMART) protein databases. Here we report the 835 unique transcripts assembled from these clones and the putative assignment of 418 of these sequences among 24 different major protein categories.
class is composed of ribosomal, mitochondrial and other housekeeping genes involved in protein synthesis. The abundance of mitochondrial and ribosomal protein coding genes is not unusual for a transcriptome analysis and illustrates the high degree of redundancy found in the libraries, especially the occurrence of numerous sequences coding for proteins involved in protein synthesis such as ribosomal RNA, e.g. 40S, 60S and other ribosomal genes. The second largest functional class includes proteins involved in energy functions of metabolism (metabolism, energy containing 163 ESTs which generated 23 concensus sequences and 47 singletons) such as NADH dehydrogenase, cytochrome c oxidases, cytochome b, adenosine triphosphate (ATP) synthase and other synthetases ( Table  1). As with proteins associated with protein machinery, proteins involved in metabolism, energy, were highly abundant. The abundance of energy facilitating proteins is a feature consistent with the active role of the midgut in cell growth and hemoglobin digestion during blood feeding.
Other notable classes of biological function include secreted proteins for which there were 9 concensus sequences and 37 singletons containing a predicted signal peptide, protein modification machinery (5 concensus sequences and 30 singletons) that contains transcripts coding for proteins involved in oxidative stress such as glutathione S-transferase (GST) and glutaredoxins, peptidase inhibitors and amino acid (aa) metabolism which includes cysteine, serine and aspartic peptidases. Included among the transcripts in the cytoskeletal category were two singletons identified as tropomyosin (DvM 201) and troponin (DvM 290). Troponin and tropomyosin together form the tropomyosin protein complex that serves as ca ++ binding proteins, especially the calmodulinlike proteins, identified as CLSP (calmodulin-like skin proteins in human skin). These proteins are members of the calmodulin family and troponins. Calmodulin is important as a signaling protein as well as a cellular regulator where it functions as a second messenger, as a regulator of calcium-dependent enzymes, and many other cellular functions. Periodic contraction of the smooth muscles surrounding the midgut is believed to be important during blood feeding.
Comparative analysis of the two cDNA libraries indicated that each library (unfed/2-day vs. 6-day-fed) were evenly represented in the combined analysis with 455 and 440 unique transcripts, respectively ( Table 1). The average number of ESTs contributing to each transcript was also similar (1. 40 and 1.58). Notable exceptions to this are the categories containing aa metabolism and lipid metabolism transcripts which contain more transcripts from the 6-day-fed midgut library than the unfed/2-day-fed library ( Table 1). Table 2 summarises the 50 most abundant transcritps (3 or more ESTs) identified from the combined cDNA library analysis. The table indicates the number of ESTs contributing to the concensus sequence, the representative EST for each concensus and the best match based on the BLASTX algorithm to the NR database and a customised database (ACARI) including all Acari protein sequences found in GenBank, and the accession number for each match. The most abundant transcript (DvM 2) comprises 480 ESTs associated with mitochondrial DNA. The second most abundant transcript (DvM 4) has an unknown function and, interestingly, appears to be secreted with a predicted signal peptide between cleavage positions 24 and 25 (VLS-QE), based on peptide comparison using the Signal P server [22]. The protein sequence for DvM 4 appears to be full length, based on the presence of a predicted signal peptide and a polyA tail preceeded by a stop codon, and has a molecular weight of 18.3 kDa and an isoelectric point (pI) of 8. 50. The third most abundant transcript (DvM 5), comprised of 28 ESTs, is associated with the metabolic lipid (ML) domain protein, important in pathogen recognition and innate immunity. The fourth most abundant transcript (DvM 6) with 22 ESTs with similarity to cytochrome oxidase 1 and the fifth most abundant transcript (DvM 7) respresented by 19 ESTs associated with cytochrome oxidase 3, are both important in mitochondrial metabolic activity. The sixth most abundant transcript represented by 16 ESTs is associated with an unknown salivary protein in Ixodes scapularis. The seventh (DvM 1) and eighth (DvM 9) most abundant transcripts (14 and 13 ESTs, respectively) contained no significant matches to the NR or ACARI database which are based on translated BLAST algorithms, but when compared with nucleotide databases such as the mitochondrial-plastid (MIT-PLA) and rRNA subset databases using BLASTN significant homologies were found with mitochondrial DNA species (indicated on Table 2 with an asterisk). The remaining unique transcripts comprised fewer sequences; most (62%) had 5 or less ESTs. Twenty-nine transcripts contained homologies to housekeeping proteins, including 11 concensus sequences with homologies to RNA structure, RNA binding, translation and transcription, and nine transcripts appear to be involved in energy metabolism. When matched against the ACARI and CDD databases, most of the abundant transcripts (66%) showed the highest matches to ticks or other acarines. Three transcripts were recognised as cysteine peptidases (DvM 12, 13, and 42) with close matches to similar peptidases found in R. haemaphysaloides, R. appendiculatus and H. longicornis. One transcript (DvM 10) was recognised as a GST with a very high match to a D. variabilis midgut GST; another (DvM 20) was tentatively assigned as a mucin glycoprotein. Eleven transcripts contained unknown sequences with no functional relationship to known proteins or showed conflicting matches with low E-values and, consequently, could not be assigned a function.

Categories of putative functions involved in tick midgut function
Eighty-three transcripts (23 concensus sequences and 57 singletons) were identified as proteins putatively involved directly in blood-meal digestion by D. variabilis, based on putative biological function. These include enzymes involved in 1) oxidative stress reduction/antimicrobial activity/detoxification (17 transcripts); 2) peptidase inhibitors (9 transcripts); 3) protein digestion (cysteine-, aspartic-, serine-, and metallo-peptidases) (26 transcripts); 4) cell, protein and lipid binding, including mucins (11 transcripts); 5) carbohydrate digestion (4 transcripts); 6) immunity (8 transcripts); 7) iron/heme metabolism and transport (3 transcripts); and 8) secreted proteins (5 transcriptss). With the exception of metallopeptidases, secreted proteins and transcripts associated with lipid function and iron/heme metabolism and transport, all categories showed putative increased expression during blood feeding (Table 3 and Figure 1). Table 3 sum- marises the major groups involved in blood feeding and digestion. Each category will be discussed in detail below. Table 4 lists the 4 concensus sequences and 12 singletons that contained transcripts for proteins expressed in response to oxidative stress, antimicrobial activity or detoxification associated with blood feeding. Most were found in the midguts from 6-day-fed ticks (n = 23, 75%). GST comprised the most common members of this category. Seven putative GST were identified (DvM 10, 102 164, 277, 286, 404 and 695), six of which match GST from other tick species. With but one exception (described below), all were found in the midguts from the 6-day-fed ticks and lacked signal peptides, suggesting they are most likely cytoplasmic proteins. Several of the GST-like transcripts (DvM 10, 102, 286 and 277) are probably not novel because they show excellent matches (99% identity) to GST from D. variabilis (AA092279.1) and Rhipicephalus (Boophilus) microplus (AAD15991.1). The identity of DvM 10 was also confirmed by tryptic digestion/mass spectrometry ( Figure 2). Phylogenetic analysis comparing published GST sequences from non-insect arthropods to those found in this study indicated that DvM 10 and 404 belong to the cytoplasmic GST class Theta (delta/epsilon), whereas DvM 102 and 164 are most closely related to the cytoplasmic Mu class ( Figure 3) [23]. Alignment of GST from various tick species supports the phylogenetic placement of our transcripts ( Figure 4). Several conserved characteristics also support the phylogenetic placement of these transcripts; DvM 10 (DvM 404, a singleton, was 5' truncated and therefore could not be analysed) contains the hallmark of a Theta class GST with a catalytically essential serine rather then a tyrosine in the N-terminus; the SMAIL/TRAIL conserved motif; and several conserved aa involved in the GST fold [24] (Figure 4). Previous work [24] identified two GST from D. variabilis both belonging to the Theta class. This is the first identification of GST from D. variabilis belonging to another cytoplasmic GST family, namely the Mu class. The phylogenetic tree supports the functional assignment of these transcripts as GST. GST are known to play an important role in cellular stress responses such as may occur as a result of blood feeding as well as in innate immunity [24][25][26][27].

Oxidative stress, oxidase-related antimicrobial activity or detoxification
The last GST, DvM 695, a peptide represented by a single EST found in the unfed/2-day-fed midguts, does not match any tick or acarine species. Rather, it shows a match to a GST from Strongylocentrotus purpuratus and appears to be a microsomal GST3 (MGST). The microsomal GST superfamily, termed MAPEG (membrane-associated proteins in eicosanoid and glutathione metabolism) [25], is a glutathione transferase as well as a glutathione-dependent peroxidase. There are six families of MGST including MGST1, 2, and 3, leukotriene C4 synthase (LTC4), 5lipoxygenase activating protein (FLAP), and prostaglandin E synthase (PGES). Insect MGST are most similar to MGST1 and PGES, yet DvM 695 appears to be most related to MGST3 based on phylogenetic analysis ( Figure  5a) and multiple pairwise alignment (Figure 5b) [26]. D. variabilis DvM 695 appears to be the first MGST identified from a tick.
Two transcripts, DvM 235 and 509, each a singleton from the 6-day-fed and unfed/2-day-fed libraries, respectively (Table 4), appear to be antioxidants known as thioredoxins (TRX) which facilitate the reduction of other proteins by cysteine thiol-disulfide exchange (for review see [27]). While thioredoxins are found in nearly all known organisms, only one tick thioredoxin has been deposited in GenBank (AAV63537.1). BLAST analysis of DvM 235 against the NR database revealed a high similarity (Evalue 4e-038) to an I. scapularis "tick-fed salivary protein 3" (AAV63537.1) identified from a salivary gland cDNA library and was found to be homologous to the thioredoxin-1 protein [28]. This sequence along with DvM 235 was found in the same major clade with other arthropod and non-insect arthropod thioredoxin proteins ( Figure  6a) and more specifically, in a sub-clade with a thioredoxin from I. scapularis, mentioned previously, and a scorpion thioredoxin (Mesobuthus cyprius, CAE54120.1). Additionally, the TRX found from ticks contains the characteristic and essential CXXC motif containing the two vicinal cysteines that enable thioredoxins to reduce other proteins ( Figure 6b). In addition to the antioxidant functions of the thioredoxin family, thioredoxin-1, it has been shown that when secreted by antigen presenting cells it is a potent co-stimulator for T-cell activation and growth, and thus is involved in immune functions [29]. DvM 235 appears to be the first thioredoxin found in D. variabilis and is putatively assigned to the TRX-1 subfamily. DvM 509 was excluded from subsequent phylogenetic analysis due to N-terminal sequence truncation.
One transcript (DvM 401), a singleton, found in the 6day-fed midgut library, was found to be homologous to another antioxidant, glutaredoxin (GRX), which is both structurally and functionally related to TRXs (For review see [27]). In vertebrates, three Grx genes have been characterised; GRX1 which is primarily cytoplasmic, GRX2 contain nuclear and mitochondrial variants and GRX5, which is primarily localised in the mitochondria. Some members of the GRX2 group contain a single cysteine residue at the putative active site, whereas like all TRX members, other members of the GRX superfamily have a CXXC cysteine motif. DvM 401 was found in the clade with other GRX2 members ( Figure 7). No GRX sequences from acarines were found on GenBank, yet our transcript appears to cluster with other arthropods including an Aedes aegypti glutaredoxin (EAT33643.1) to which it is most homologous (Figure 7). Additionally, DvM 401 contains the catalytic site motif, CXXC (data not shown). In ticks, GRX may be involved in trapping reactive oxygen species that would otherwise interact with cellular thiols.
Another transcript (DvM 122) found in the oxidative stress related group was found only in the unfed/2-day-fed midgut library of which the deduced aa sequence appears to be homologous to a phospholipid-hydroperoxide glutathione peroxidase (PHGPx) from Rhipicephalus (Boophilus) microplus (94% identity) ( Figure 8). PHGPx, along with glutathione peroxidase (GPx) are selenoenzymes that catalyse the reduction of hydroperoxides in the presence of glutathione [30]. Multiple pairwise alignment of DvM 122 to R. microplus PHGPx illustrates the conserved features of this protein such as the codon TAG coding for selenocysteine and the two active site aa (Gln and Trp) which interact with selenocysteine ( Figure 8) [31].
Differential display of proteins associated with midgut function either unfed and 2 days post bloodmeal (unfed/2 d fed) or 6 days post bloodmeal (6 d fed)    The tick midgut also shows the presence of enzymes that function as antioxidants by scavenging free radicals known as superoxide dismutase (SOD). One SOD was identified in DvM 199 a singleton expressed in the 6-dayfed midgut library. DvM 199 shared significant identity with Cu, ZnSODs from various species, including a salivary gland specific Cu, ZnSOD from I. scapularis. Cu, ZnSODs catalyse superoxide anion into oxygen and hydrogen peroxide by the reduction and oxidation of a metal ion which constitutes the catalytically active redox center [32]. Cu, ZnSOD is important for protection against exogenous oxidative stress by converting superoxide radicals to molecular oxygen. Based on metal binding patterns and signature sequence patterns, DvM 199 appears to be a member of the SOD1 subfamily of superoxide dismutases [33] (Figure 9). Interestingly, Cu, ZnSOD from the bacterium Haemophilus ducreyi, a gramnegative heme obligate coccobacillus, appears to bind heme [34,35]. This suggests that this enzyme, in addition to its antioxidant properties, could function in heme trafficking that would be important in the intracellular tick bloodmeal digestion process.
Transcripts for other oxidative stress peptides include a metallothionen (DvM 22), which may be involved in chelating heavy metals, a selenoprotein (DvM 143), a protein disulfide isomerase (DvM 258), and an aldehyde dehydrogenase (DvM 453) that may function to detoxify aldehydes, such as toxic byproducts resulting from lipid peroxidation (aldehyde detoxification) and may be involved in oxidoreductase activity. The deduced amino acid sequence of DvM 556 shows significant similarity to a quinoid dihydropteridine reductase from Gallus gallus (NP_001006566.1, 7E-076 e-value). Quinoid dihydropteridine reductase has oxido-reductase activity involved in tetrahydrobiopterin biosysnthesis and amino acid transport and metabolism. Table 5 shows 9 unique transcripts, 8 of which are singletons, found to be associated with peptidase inhibitors. Of special interest is the finding that three of the peptidase inhibitors were found only in the unfed/2-day-fed midguts. DvM 626, a putative secreted peptide, showed a match to a similar serpin from the cattle tick, R. microplus, known as boophilin, and includes the Kunitz-type trypsin inhibitor domain. DvM 544, a predicted cytoplasmic peptide, also shows the Kunitz-type domain, strongly supporting its role as a serpin despite its poor match in the ACARI and BLAST (NR) databases. DvM 602, another predicted cytoplasmic peptide, is a cystatin with the characteristic cystatin domain. The remaining peptidase inhibitors were found exclusively in the 6-day midguts; four are putative cytoplasmic peptides while the location for the other two could not be determined by the Signal P server.

Peptidase inhibitors
Two transcripts contained significant matches to serine peptidase inhibitors known as serpins, DvM 422 with 1 EST and 78 with two ESTs, all expressed in 6-day-fed midguts (Table 5). Serpins are important regulators of serine peptidases involved in inflammation, blood coagulation, fibrinolysis and complement activation [36]. Serine peptidase inhibitors include members of the Kazal, Kunitz, αmacroglobin and serpin families. Serine peptidase inhibitors function in insect hemolymph for protection from SDS-PAGE protein gel from a lysate of midguts from 6 d-fed female Dermacentor variabilis showing the location of proteins identified by tryptic digestion-mass spectrometry infection by pathogens or parasites [37]. DvM 422 contains a full-length sequence and is most closely related to Lospin 1, 2, and 3 from Amblyomma americanum [38] that are three of 17 serpins found in the Lone Star tick ( Figure  10). In A. americanum serpins are expressed ubiquitously in the midgut, salivary glands and ovaries with Lospin 1, 2, and 3 having the greatest expression in the midgut [38]. Serpins contain a conserved domain (cd00172) and a reactive center loop, [GREV]- [FRADHP], which is conserved among ticks including our transcript (data not shown). DvM 78 is 5' truncated yet it contained a significant match to a serpin from H. longicornis (BAD11156).
Two singletons (DvM 312 and 626) contained a significant match to a protein named boophilin identified from the cattle tick, R. microplus (CAC82583). Although not definitively characterised, boophilin appears to be related to a thrombin inhibitor [39]. Similar to boophilin, both transcripts contain two conserved Kunitz domains (cd00109) and are closely related to a conserved domain for BPTI (bovine pancreatic trypsin inhibitor)/Kunitz family of serine peptidase inhibitors. This domain contains a characteristic disulfide-rich alpha+beta fold as well as a trypsin interaction site ([PCRAMXS]). DvM 312 and 626 contain two Kunitz domains and 6 cysteine residues that together create three disulfide bridges, although DvM 312 is 5' truncated, therefore the first three cysteines of the first domain are absent ( Figure 11). A thrombin inhibitor has been identified and functionally characterised from one hard tick, Amblyomma hebraeum (Amblin, AAR97367) [40] and two soft tick, Ornithodoros moubata (Ornithodorin, P56409) [41] and O. savignyi, (Savignin, AAL37210) [42]. The prototype for this family, BPTI, contains two recognition loops, the first of which contains a single aa (Lys15) that is the principle determinant of inhibitor specificity. Polymorphisms in these loops contribute to individual species specificity; BPTI inhibits trypsins and boophilin, ambilin and ornithodorin inhibit thrombin. The exact mechanism through which thrombin is inhibited is not understood for hard ticks. The binding appears to be novel in soft ticks, such that neither of the reactive site loops contact the peptidase in the Ornithodorin-thrombin complex; rather, the interaction is through the N-terminal residues [41,42]. It is unknown if the two proteins identified from D. variabilis are, in fact, thrombin inhibitors and, if so, if they bind in the same manner as Ornithodorin. Preliminary examination of the sequences obtained from D. variabilis suggests an alternative method.
Deduced aa sequences of three singletons, DvM 226, 334, and 602 shared identity to cysteine peptidase known as cystatins. All three consensus sequences were truncated at the N-terminus; thus complete sequences could not be evaluated. DvM 226 appears to be identical to DvM 334, yet is significantly more truncated and thus is not represented in the alignments or phylogenetic analysis. Based on multiple pairwise alignment and phylogenetic analysis, there appears to be two cytoplasmic and one secreted cystatin found in the cDNA libraries from D. variabilis midguts ( Figure 12). DvM 602 appears to be most related to R. microplus putative intracellular cystatin (ABG36931.1) and I. scapularis cytoplasmic cystatin (AAY66864). Although the aminoterminal region is missing, based on phylogenetic similarity we can presume that DvM 602 is a cytoplasmic cystatin (Figure 12a, c). Unlike secreted cystatins, intracellular cystatins do not present with predicted disulfide bonds which is observed among our putative cytoplasmic transcripts ( Figure 12c). DvM 334 appears to be a secreted cystatin based on phylogenetic analysis (Figure 12a, c). Grunclova et al. [    MAP PNLPYYIDGDVKLTQSMAILRYLARKHG LGSLALIGLMGTTVFSAFQHLGWVKTGLGGGSKCCH- Analysis of Thioredoxin (TRX) protein family  other known cystatins [44] such that the molecule has three papain-binding areas and four conserved cysteines that create two disulfide bridges (Figure 12b). The three papain-binding areas are thought to create a wedgeshaped binding site involved in reversible binding in the active site of cystatin peptidase of the papain family [44]. Grunclova et al. [43] found that the gut specific O. moubata and midgut I. ricinus cystatins shared the third papain-binding site, characterised by a PW hairpin loop. This was not seen among salivary gland I. scapularis cystatins but we find this motif in the midgut-specific D. variabilis DvM 334 (Figure 12b). In all cystatins from D. variabilis, the QNVLG or QVVAG domain is conserved as in other cystatins (Figure 12a, b). Cystatins are important in disrupting the activity of cysteine peptidases, enzymes that are essential for several pathogenic parasites and bacteria. Thus, cystatins not only have the capacity to regulate normal biological processes but may also participate in the defense against microbial infections [45].

Peptidases
Peptidases comprise the largest number of putative expressed genes associated with bloodmeal digestion. Twenty-six transcripts consisting of 38 ESTs were divided among four major groups of pepidases found in the midgut of D. variabilis; serine, aspartic, cysteine and metallo ( Table 6).

Serine peptidases
Trypsins and chymotrypsins are the most extensively studied digestive serine peptidases in haematophagous insects. Five transcripts were found that matched serine peptidases, all found only in the 6-day-fed midguts. Three transcripts (DvM 60, 210, and 330) showed high levels of similarity to serine peptidases from other tick species. All three transcripts were truncated at the aminoterminus, thus no secretion potential could be evaluated. Miyoshi et al [17] described a serine peptidase from H. longicornis (AB127388) that contained the three conserved catalytic aa typical for chymotrypsin-like proteins (His-Asp-Ser). Alignment of DvM 60, 210 and 330 with H. longicornis and other tick serine peptidases from GenBank revealed the extent of the 5' truncation of the three D. variabilis transcripts, yet for DvM 210 the second (D) and third (S) catalytic aa in the trypsin catalytic triad were conserved ( Figure 13). Additionally, although we were only able to sequence the 3' fragments of the protein, DvM 60 contains the conserved serine whereas DvM 330 contained an isoleucine in place of the serine. As seen in other hemotophogus arthropods [46], it may be possible that some of the serine peptidases found in the tick midgut may be associated with immunity rather then digestive function.
Two transcripts (DvM 283 and 394) were found to be most closely related to serine carboxypeptidases. Serine carboxypeptidases (SCP) are proteolytic enzymes that exploit serine in their catalytic activity, as with chymotrypsins, SCP have a catalytic triad of serine, aspartate and histidine (SDH) whereas chymotrypsins have the HDS triad, which catalyses hydrolysis of C-terminal residues in peptides and proteins as acidic pH. A SCP from H. longicornis (BAF64246.1) was described by Motobu et al. [47], which contained the catalytic triad at positions 178, 450 and 397. Alignment of DvM 238 with a SCP from H. longicornis, a salivary SCP from I. scapularis and a SCP from the jewel wasp, Nasonia vitripennis illustrates that, although truncated at the N-terminus, DvM 238 contains the second (Asp) and third (His) aa of the triad (data not shown). Without further analysis of the full-gene product, it is impossible to determine whether the first catalytic aa is conserved. Based on identity with N. vitripennis (E-value 7e-24), it seems probable that DvM 283 and DvM 394 are midgut serine carboxypeptidases.

Aspartic peptidases
Three transcripts putatively assigned as aspartic peptidases were identified in the midgut libraries. Aspartic peptidases are a family of proteins that include pepsins, cathepsin D, cathepsin E and renins, and are believed to be important in hemoglobin proteolysis [48]. These enzymes are involved in degradation of intracellular and endocytosed proteins and thus have been implicated in blood meal digestion in some ectoparasites, such as mites [49] and ticks [46]. Aspartic peptidases have also been implicated    in hemoglobin (Hb) proteolysis [50][51][52]. Among ticks, an aspartic peptidase named BYC from R. microplus appears to be involved in vitellin (yolk protein) digestion as well as heme binding [53]. We identified transcripts similar to an aspartic peptidase, cathepsin D (Table 6).

Analysis of Glutaredoxin (GRX) protein family
Three transcripts (DvM 108, 249, and 254) contained significant matches to a peptidase in H. longicornis named longepsin (BAE53722.1), which is known to cleave hemoglobin. All three transcripts were found only in the midguts from 6-day-fed ticks; no clones were found in unfed or 2-day-fed ticks. DvM 249 and 254 were extensively 5' truncated, thus were removed from phylogenetic analysis (Figure 14a). DvM 108 and 249 are probably aspartic peptidases since they have an aspartic acid domain, i.e., Asp-Thr-Gly (DTG) catalytic site motif also found in H. longicornis [54] and several other cathepsin D peptidases necessary for its enzymatic activity ( Figure  14b). This enzyme is typically found in lysosomes. Boldbaatar et al. [54] suggest that in H. longicornis, this enzyme "plays an integral role in the proteolysis of erythrocyte Hb obtained from a host blood meal." The occurrence of a similar aspartic peptidase in the D. variabilis midgut suggests that it also is likely associated with hemoglobin digestion. Phylogenetic analysis revealed that DvM 108 is most closely related to H. longicornis aspartic peptidase and is found in the same sub-clade as other tick cathepsin-D proteins (I. ricinus and R. microplus), and is also within a major clade containing other arthropod cathepsins (Figure 14a).

Cysteine peptidases
Fourteen transcripts were found, comprising either multiple or single sequences, that matched cysteine peptidases in the ACARI and/or NR databases and at least one of the CDD databases. Of the 24 total EST containing homology to cysteine peptidases, 19 ESTs were found in the 6-dayfed midguts, whereas only 5 ESTs were found in the 2-dayfed library, suggesting that the expression of this protein family is induced during feeding (Table 6). Phylogenetic analysis revealed three major groups of cysteine peptidases identified among the two cDNA libraries; legumainlike, cathepsin B-like and cathepsin L-like ( Figure 15a and Figure 16a).
DvM 62, 96, and 694 share significant sequence similarity to a legumain-like protease from I. ricinus. Legumain-like proteases are members of the cystein peptidase family (Clan CD, Family C13) and act specifically as asparaginyl endopeptidases with strict cleavage specificity. Asparaginyl endopeptidases (AE) appear to process other proteins and have been found to be involved in peptide processing before MHC-II loading [55], protein processing during seed germination, and, possibly the most relevant to the hematophagous behavior of ticks, AE have been shown to activate cathepsin zymogens in the gut of blood feeding helminthes such as Schistosoma mansoni -allowing Hb digestion [56]. Recently, AE orthologs have been described in two hard ticks, I. ricinus [50] and H. longicornis [51]. Each has been shown to function as hemoglobinase. Of the three transcripts found in the D. variabilis library, two (DvM 62 and 96) appear to be 5' truncated thus were removed from phylogenetic analysis. The third transcript, DvM 694, appears to be full length and contains a signal peptide (VAA-AP), indicating its likely secretion from the cell. DvM 694 shares 69% identity with I. ricinus (AAS94231.1) and 74% identity with H. longicornis (BAF51711.1) tick legumain and is found in a clade with other known tick-derived AE (Figure 15a). Alignment of the three known tick AE is shown in Figure 15b. The residues His and Cys, involved in forming the catalytic dyad of AE, are conserved among all three ticks including the transcript identified in this analysis (Figure 15b). DvM 62 and 96 each contain two ESTs found in the six days postattachment midguts, whereas DvM 694 is a singleton expressed in the midgut of unfed or 2-day-fed ticks. The three transcripts share 97% aa similarity with only five aa differences between them; yet without the entire sequence it is impossible to know if the three share a similar function. Potential differences in the N-terminus could Based on homology to known proteins, DvM 13 contains a predicted signal cleavage site (TTA-AS) suggesting secretion from the cell (data not shown). Multiple sequence alignment of tick cysteine peptidases indicated that the aa involved in the catalytic dyad (Cys and His), which are present in all papain-like cysteine peptidases, were conserved among the tick species, with the exception of DvM 542, which did not contain Cys (Figure 16b). It has been shown that two other residues play an important role in catalysis, a Gln preceding the catalytic Cys, believed to help in the formation of the oxyanion hole, and an Asn residue which orients the imidazolium ring of the catalytic His. As with the catalytic dyad, Gln and Cys were also conserved among the D. variabilis transcripts. Although there was little homology among the entire length of sequences, the residues surrounding the catalytic aa were equally conserved (Figure 16b).

Metallopeptidases
Four putative metallopeptidases were found among the transcripts. All were found only in the midguts from unfed/2-day-fed ticks. Results from the NR and GO database identified a PA2G4-like (Proliferation Associated Protein 2G4) conserved domain in DvM 732, whereas a match to a metallopeptidase was identified based on a search of the KOG database (E-value 3e-012). PA2G4 is related to an aminopeptidase M which is implicated in cell-cycle control. One metallopeptidase, DvM 594, was homologous to an I. scapularis salivary gland secreted protein, Is6 (AAO85923.1), based on searches of the NR and ACARI databases. DvM 806, related to a metallopeptidase, is homologous to a membrane-type 1 matrix metalloproteinase cytoplasmic tail binding protein-1 (E-value 3e-009) based on comparison to the NR database. A final metallopeptidase, DvM 675, appears to have mitochondrial processing peptidase activity and is related enzymes in the insulinase super family (Clan ME, Family M16) based on the best match to the KOG database (E-value 2e-062). In all four examples, the protein appears to be truncated, thus functional active sites indicative of metallopeptidases remain to be confirmed.    Table 8 lists the 11 transcripts for proteins probably associated with cell, protein and lipid binding functions. In contrast to the other protein classes, most transcripts in this category contained sequences from both the 6-dayfed and unfed/2-day-fed midguts. Included were four glycine rich proteins which appear to be most similar to salivary cement or glycine rich proteins, two BM86-like surface antigens, four mucin like proteins and a single transcript for a tick receptor outer surface protein A (TRO-SPA).   The most abundant group associated with lipid binding contains four transcripts comprised of nine EST and is homologous to mucins. DvM 827 and 635 contain a putative secretory peptide while DvM 718 and 20 appear to be cytoplasmic proteins likely found on the cell membranes.

Analysis of Boophilin-like peptidase inhibitors
Mucins are important in coating the lining epithelium of the gut, which contributes to their role as mucosal barriers. DvM 827 and 635 share identity with a conserved domain, CBM_14, a chitin binding peritrophin-A domain characterised by an extracellular domain that contains six conserved cysteines, forming three disulfide bridges (Figure 17b). DvM 20, derived from six ESTs, found in both the unfed/2-day-fed and 6-day-fed midguts, also shows a match to an allergen-like protein from the dust mite, Dermatophagoides farinae. However, this sequence contains a conserved domain (Pfam01456) similar to mucin-like glycoproteins in the midgut peritrophic membrane of insects [52]. DvM 718, with one sequence found only in the unfed/2-day-fed midguts, shows a match to a mucinlike peritrophin sequence from the soft tick O. moubata as well as the chitin-binding Peritrophin-A domain, a characteristic feature of the peritrophic membrane ( Figure  17a). The acellular peritrophic membrane, which forms within as little as 9 -12 h after the commencement of feeding [57] lies close to the luminal surface of the epithelium where it protects the gut against injurious particulates and ingested microbes. It has been described from several species of ticks [58,59]. While DvM 718, 827 and 635 are closely related to other tick mucins, it is interesting to note how similar the mucins from D. variabilis midguts are with putative peritrophins from two sand fly species, Lutzomyia longipalpis and Phlebotomus papatasi (Figure 17a).
Glycine rich proteins were also abundant in this midgut category. Three of these putative proteins, DvM 50, 527 and 613, were found only in the unfed/2-day-fed midguts, while the fourth, DvM 257, was found only in the 6-dayfed midguts. DvM 613 was also a secreted protein. Each of the glycine rich proteins was similar to tick salivary gland cement-like proteins. Tick cement proteins are characterised by glycine rich aa repeats that occur as GLG [G/Y/S/F] tripeptides and may also show a GSPLSGF septapeptide [60]. All four of the putative glycine rich proteins showed variations of the tripeptides; DvM 257 also contained the septapeptide. DvM 257 showed 52% identity with RIM36, a cement protein from the salivary glands of R. appendiculatus (AAK98794.1) that contributes to the formation of the attachment cement. In contrast, DvM 527 and 613 showed the highest similarities, 39% and 40%, respectively, to a similar glycine rich cement protein from I. scapularis. The role of glycine rich proteins in the tick midgut is currently unknown.
Several transcripts were tentatively identified as membrane surface receptors/antigens. Two transcripts (DvM 70 and 558), show a match to Bm86, a membrane-bound surface protein from Hyalomma anatolicum (AAL36024.1) as well as Bm86 homologues from R. microplus, H. longicornis and R. sanguineus. Bm86 is similar to mammalian angiotensin-converting enzyme and, therefore, may function in a similar role in ticks [61]. Both appear to be glycoproteins; DvM 558 also shows a match for the von Willebrand factor, which contributes to platelet (thrombocyte) clumping. Both transcripts are 5' truncated by approximately 400 aa, yet along the approximately 232 aa of the 3' ends they are considerably conserved to other Bm86-like proteins found in ticks, particularly along the cysteine framework (data not shown).
A noteworthy finding was DvM 708, which showed a match for TROSPA, the I. scapularis midgut cell surface protein that binds to Borrelia burgdorferi spirochetes. This protein was found only in the unfed/2-day-fed ticks. Although the match is relatively poor, this finding may merit further study. To date, TROSPA has only been reported from I. scapularis [62].

Transcripts related to Immunity within the midgut
Eight transcritps contained proteins putatively involved in immunity in the gut of the tick ( Table 9). The most abundant transcripts in this group are putative allergen-like proteins containing ML domains ( Figure 18). Two (DvM 5 and 90) of the five transcripts associated with allergenlike proteins were found in both the unfed/2-day-fed and 6-day-fed midguts, while DvM 339 and 378, both singletons, were expressed only in the 6-day-fed midguts; DvM 537, a singleton, was found in the unfed/2-day-fed midguts. DvM 90, present in both the unfed/2-day-fed and 6day-fed midguts, is a secreted protein. The others are cytoplasmic or of indeterminate status. All five transcripts showed a match for the ML lipid recognition domain and all match allergen-like proteins or ML domains from other tick species, namely I. ricinus (AAP84098), which was found to be induced by a Borrelia infected bloodmeal in the midgut of this tick [63]. DvM 90, 339, 378, and 5 share significant homology with E1_DerP2_DerF2 protein domain (Pfam02221, E1_DerP2_DerF2) belonging to a family of ML domain-containing proteins that is a lipid recognition domain found in plants, fungi, animals and also includes the dust mite allergen Der P 2. These transcripts appear to code for a protein similar to the Dermatophagoides pteronyssius mite allergen (Pfam02221, DerP2_DerF2, ML domain), a lipid-binding protein which had the closest match to a similar protein in Ixodes ricinus, and other proteins of unknown function. These proteins are implicated in pathogen recognition, particularly recognition of pathogen-related lipids and involved in innate immunity and lipid metabolism [20]. Two transcripts, DvM 90 and 5, contain a ML lipid recognition domain also present in Niemann-Pick type C2 (Npc2)type proteins and the phosphatidylinositol/phosphati-dylglycerol transfer protein (PG/PI-TP). The latter is a ubiquitous cytosolic protein of eukaryotic cells that transports phospholipids from the endoplasmic reticulum and Golgi to other cell membranes [64]. Both transcripts were found in the clade with other ML domain containing acari species (Figure 18a). Allergen-like proteins are believed to be important in innate immunity by recognising and binding to lipids found on microbes, including pathogenic microbes ingested with the blood meal. Multiple pairwise alignment of tick ML domain-containing proteins revealed the conserved cysteine framework found in allergen-like proteins was also conserved in two D. variabilis derived sequences, DvM 5 and 90, as well as conserved aa involved in putative lipid binging activity (Figure 18b). In the context of the intracellular digestion of the bloodmeal, these ML-like proteins could be associated with lipid absorption form the phagolysosomes, a role that clearly needs more investigation.     The two transcripts tentatively identified as Dorin M-like proteins (DvM 224 and 231) show matches to a fibrinogen-domain containing lectin-like protein found in the hemolymph of O. moubata [65]; a similar lectin-like protein, Ixoderin, also occurs in I. ricinus. DvM 231 was found to show 25% identity to ixoderin and 22% and 24% identity, respectively, to the two lectins from O. moubata. These proteins are similar to fibrinogens and show the characteristic fibrinogen domain [66]. Notably, Ixoderin was also found in the midgut of I. ricinus [66]. DvM 231 also contained a signal peptide, similar to the other tick, insect and human lectins that were compared. This transcript was confirmed as a Dorin-M lectin by tryptic digestion/mass spectrometry (Figure 2). A second transcript (DvM 224) tentatively identified as a lectin, showed little similarity to any of the known lectins; its identity is uncertain. Lectins are believed to play an important role in antimicrobial activity in the hemolymph of ticks [66,67] as well as in the midgut of many blood-feeding insects [68].

Analysis of serine peptidases
The last protein we can include in this group is DvM 97, which is similar to the macrophage migration inhibitory factor (MIF) also found in the tick, Amblyomma americanum (E-value 3E-049), as well as many other invertebrates. This protein was found in both the unfed/2-dayfed and 6-day-fed ticks. MIF proteins have dopachrome isomerase activity, a function in arthropods provided by members of the Yellow family which is involved in melanization [69].

Transcripts related to iron/heme metabolism and transport
Two transcripts tentatively identified as ferritins were recognised, both were found only in the unfed/2-day-fed midguts (Table 10) ( Figure 19). DvM 56, with 3 ESTs, is a predicted secreted protein, while DvM 131, with 2 ESTs, is a predicted cytoplasmic protein. Both show an excellent match to similar sequences from D. andersoni and D. variabilis, as well as the conserved ferritin domain (cd00904). Ferritin is important as an iron storage reservoir and in protection against iron overload. Mosquitoes, for example, synthesise and secrete ferritin in response to iron exposure in direct relationship to iron dose [70]. A tick heavy chain ferritin was recently shown by Mulenga et al. [71] to be upregulated in response to mechanical injury and bacterial infection, thus suggesting its role in antimicrobial activity. Phylogenetic analysis of DvM 131 and 56 reveal the conserved nature of ferritins among tick species (Figure 19a and 19b). DvM 131 is found in the clade containing other Dermacentor species and is highly similar to a published ferritin from D. variabilis (AAL75582.1); therefore, this transcript does not appear to be a novel ferritin (Figure 19a). DvM 56 is found in the same clade as a horseshoe crab (Carcinoscorpius rotundicauda) ferritin which is ancestral to the tick-derived ferritins (Figure 19a).
The placement of DvM 56 in this clade, yet separate from arthropod light chain ferritins, suggests that it is either a novel ferritin or is involved in a unique function, not previously identified. The conserved aa involved in the ferroxidase diiron center is conserved among the tick ferritins excluding DvM 56, in which the second aa of the domain is a lysine rather than a tyrosine, which may contribute to the divergence from other tick ferritins ( Figure  19b). DvM 352 is tentatively assigned as an erythrocytebinding protein, although the match is poor (E-value 0.027). Another transcript, DvM 342, tentatively assigned as a housekeeping protein, may actually function in erythrocyte binding since it shows a good match (E-value 1E-016) to the clathrin adaptor protein in D. variabilis and to the clathrin adapter domain in similar proteins found in insects and ticks. Clathrin-coated pits are essential for the binding and internalisation of hemoglobin by pinocytosis [72].

Secreted proteins similar to tick salivary proteins
Five transcripts were similar to proteins secreted in the saliva of ticks. Each transcript contained a significant match to a protein identified from a tissue-specific cDNA library of dissected salivary glands. DvM 682, 830, 551, and 134 were found only in the unfed/2-day-fed midguts, whereas DvM 64 was found in the 6-day-fed guts. Two transcripts (DvM 682 and 134) had clear signal peptides, whereas the putative secretion of DvM 830, 551 and 64 is based on homology to other known secreted proteins.

Unknown, unassigned transcripts
This group comprised transcripts that had low confidence matches in the NR and/or ACARI databases, or both, or had conflicting tentative assignments with relatively low matches. Although many were short and incomplete sequences, others were long or appeared to be complete sequences and may represent novel genes. Many (DvM 37) were secreted proteins. The reader may access these sequences for further study accessing the the supplemental data given in the Methods section of this report.

Protein identifications
Tryptic digestion/mass spectrometry (mass fingerprinting) (Figure 2) provided supporting evidence for the functional assignment of the following transcripts found in the midgut library: 1) 70 kD heat shock protein; 2) GST (D. sequencing facility). The latter is noteworthy in view of reports of the role of the female tick midgut as a secondary site of synthesis of vitellogenin, a known hemelipoglycoprotein, as well as in the fat body [73]. Attempts to identify proteins isolated from PVDF blots by Edman degradation were unsuccessful because they were N-terminally blocked.

Conclusion
In this study, we constructed a PCR-based cDNA library from the midguts of unfed/2-day-fed and 6-day-fed virgin females of the tick D. variabilis and analysed 1,679 highquality randomly sequenced ESTs. We obtained partial or full-length information on proteins and peptides, most of which appear to be novel. No transcripts were found from rabbits, the host on which the ticks had been fed. In addition to functional assignments based on the criteria described previously, we confirmed the identity of seven proteins by tryptic digestion/mass fingerprinting of bands eluted from SDS-PAGE gels of midgut extracts, as well as four other proteins for which no transcripts were found.
Comparison of the transcripts from the unfed/2-day-fed versus the 6-day-fed ticks indicates that most of the sequences were found in the latter; few were found in both. This was especially true for the peptidases; 17 of the 26 transcripts in this category were expressed in the 6-dayfed midguts, and only three appeared in both. The same pattern is evident for the peptidase inhibitors (6 versus 3), hydrolases (6 versus 1) and oxidative stress proteins (12 versus 4, with only 1 found in both). This is not surprising, since little blood is imbibed during the first two days after attachment. However, several functionally important proteins and peptides were found to have been expressed in the early feeding period, especially 1) the cell/protein/ lipid-binding proteins that include erythrocyte and hemoglobin-binding proteins; eight of these were found in the unfed/2-day-fed midguts and one were found in both; 2) peritrophin, responsible for formation of the peritrophic 7.E-18 *Accession number represents transcripts derived from this analysis and submitted to Genbank.   membrane, but absent in the later feeding period; and 3) cysteine and metallo-peptidases, peptidase inhibitors and oxidative stress proteins, many of which may have an antimicrobial role.

Analysis of mucins
The library shows a remarkable degree of redundancy, a finding previously reported for the salivary gland cDNA library [74][75][76]. Especially noteworthy is the large number of cysteine and serine peptidases, serpins, hydrolases, GSTs, dehydrogenase and other free-radical reducing enzymes, and the numerous binding proteins. Such duplication is consistent with the finding of extensive gene duplication for genes of great functional value in the blood feeding process, as suggested by Ribeiro et al. [77]. Only 58 of the 835 (6.9%) transcripts showed signal peptides, indicating that most were involved in intracellular processes in contrast to the salivary glands, where a much higher proportion (29%) comprised secreted proteins [77,78]. Less than half had functional assignments based on the criteria described above. The large number of peptidases and peptidase inhibitors is consistent with the intracellular digestive processes characteristic of these ticks.
As might be expected, the largest category of transcripts in the library, with 289 transcripts, comprised the housekeeping proteins, subdivided into a least 23 functional groups. Most represented transcripts for RNA structural proteins, transcription/translational activity, metabolism, cellular and mitochondrial oxidative respiration, antioxidant activity, proteasome machinery, and other housekeeping activities. The remaining non-housekeeping proteins were much less numerous. Of special interest are the proteins concerned with blood-meal digestion, especially the peptidases and peptidase inhibitors. When ticks feed and ingest blood, the hemoglobin liberated from lysis of the erythrocytes binds to the luminal surfaces of the midgut epithelial cells. There it is absorbed and incor-porated into phagolysosomes where it is digested [72]. Studies by more recent workers have shown the presence in the tick midgut of cysteine peptidases [69], unidentified aspartic and cysteine peptidases [79] and uncharacterised cysteine and serine peptidases [80]. Aside from the serine peptidases from the midguts of R. appendiculatus and H. longicornis [16,17,81] and an aspartic peptidase from H. longicornis [54], none were sequenced or their molecular structure identified. These enzymes showed greatest activity at acid pHs, suggesting that they are lysosomal peptidases. However, none have reported as many different peptidases as were recognised in the D. variabilis cDNA midgut library described in this paper. Only four, transcrips DvM 13, 254, 314 and 594 were secreted proteins, indicating that most of these peptidases were functioning in intracellular protein digestion, presumably digestion of endocytosed hemoglobin within the digestive cells. Three of the cysteine peptidases, DvM 62, 96, and 694, included a conserved domain for the legumainlike peptidase associated with hemoglobinase, further supporting the putative role of these peptidases in bloodmeal digestion. Others, such as aspartic peptidases and serine peptidases also were found without signal peptides, suggesting they are concerned within intracellular protein digestion (primarily hemoglobin) in the phagolysosome.
Metallopeptidases are also of interest, of which four were found in the midgut library. Evidence from insects suggests that they may be important in cellular immune defense [82]. Interestingly, a metallopeptidase from the tick I. scapularis was shown to contain fibrin and fibrinogen activities, revealing yet another potential function of the metallopeptidases found here [83]. Similarities with known peptidases in other ticks, other acarines and insects were relatively low (31% or less), suggesting that most of these midgut peptidases are novel. Another noteworthy finding is the large number of transcripts known   to function as antimicrobial agents, e.g., pathogen-recognition proteins, or in a dual role, e.g., as oxidative stress reduction and innate immune peptides. In haematophagous insects, microbes ingested with the blood meal provoke an effective defense by upregulating lectins, lysozyme, defensins, cercropins and other antimicrobial peptides [78,84,85]. This study suggests that an exceptionally large number of innate immune peptides or proteins occur in the midgut. Among these are the nine different peptidase inhibitors found in the D. variabilis midgut library. Although many peptidase inhibitors have been reported from ticks, most were from the salivary glands or hemolymph. A search of the literature showed four serpins in R. appendiculatus expressed in various tick organs in addition to salivary glands and midguts [86] but only one from the midgut of H. longicornis [74]. A cystatin reported from the midguts and hemocytes of H. longicornis [75] was found to increase up to 1.8 times greater when the ticks were exposed to Babesia gibsoni or B. bovis, while the recombinant protein inhibited growth of B. bovis grown in culture. The finding of numerous transcripts for serpins and cystatins in the D. variabilis midgut suggests an important role for those proteins in innate immune defense. Other proteins expressed during blood feeding probably play a role in defense against microbial invasions. Included is the von Willebrand factor peptide, an anti-clotting factor that also occurs in I. ricinus after B. burgdorferi challenge [63], the ML-domain proteins and the lectins. ML-domain proteins function as pathogen recognition proteins. The 6-day-fed midguts were also found to contain two sequences for Dorin M lectin-like peptides. Several lectins have also been reported from ticks, including Dorin M from the hemolymph of O. moubata [65] and Ixoderin from the salivary glands and midgut of I. ricinus [67]. Lectins bind to sialic acid, hexosamines and other compounds characteristic of the cell walls of bacteria and fungi and, consequently, they are important in defence against invading microbes and preventing pathogen/parasite transmission.

Analysis of ML domain containing proteins
It has now become increasingly clear that the midgut of ticks presents a hostile environment for ingested microbes. This is evident not only because of the presence of the more familiar antimicrobial peptides (lysozyme and defensin), but also because of the expression of oxidative stress-reducing, detoxifying and lipid-or proteinbinding peptides that confer antimicrobial properties, e.g., GSTs, metallothioneins, peroxiredoxins, midgut lectins and a large number of peptidases. Microbial infection is known to cause oxidative stress, leading to upregulation of GSTs, peroxiredoxins and other oxidative stressreducing proteins [76]. Clearly, the arsenal of antimicrobial agents is considerably more extensive than just defensin or lysozyme, which are either poorly expressed or absent. Indeed, in D. variabilis, the midgut lysozyme message was not significantly upregulated by blood-feeding [87] and no evidence of either the lysozyme or defensin peptides was observed in other studies of the midgut of this tick [3], although it is strongly upregulated following the blood meal in O. moubata [88]. However, it is possible that defensin peptide was overlooked. This peptide is known to bind with a serine peptidase to form an SDS-stable complex with an apparent molecular weight > 26 kDa in the blood-sucking fly Stomoxys calcitrans [89]. In addition to the native tick proteins, fragments of hemoglobin digestion also contribute to destruction of ingested microbes [1][2][3]. Bacteria such as Bacillus subtilis, Escherischia coli and Borrelia burgdorferi, fed to D. variabilis females by capillary oral feeding were taken into the midgut, but none could be re-cultured within 24 h after exposure. When midguts of these ticks were examined by electron microscopy, intact B. burgdorferi and rodshaped bodies resembling E. coli were found in several samples [81]. Since lytic activity does not appear to be the primary antimicrobial response, it is interesting to speculate that the Dorin M-like lectin and the several secreted cysteine and aspartic peptidases noted previously may kill or at least inhibit the survival of these organisms in the midgut lumen. In contrast to D. variabilis, E. coli cells ingested into the midgut of the soft tick, O. moubata, were found to survive in the midgut lumen for up to 20 days, and were destroyed gradually only after they were endocytosed within the midgut epithelial cells [90]. Within the midgut lining cells, the upregulation of lectins or lectinlike proteins, numerous GSTs, aldehyde dehydrogenase, metallothionein, SOD and other oxidative stress enzymes in response to hemoglobin uptake and digestion would also contribute to the destruction of invasive microbes.
The authors recognise that the cDNA midgut library is an exploratory catalogue of transcripts expressed in this tissue in feeding females and is most likely incomplete. Although functional assignments could be made for approximately 45% of the concensus sequences and singletons, the remainder could not be assigned, often because they were not full-length sequences. Other classes of proteins and peptide transcripts previously reported in the midgut were not recognised, e.g., defensin [3,83], lysozyme [87], heme transferases and integrins. This annotated catalogue of midgut transcripts from the midgut of a blood-fed hard tick may be useful to scientists wishing to investigate the role of tick midgut in bloodmeal digestion as well as its ability to cope with oxidative stress, antimicrobial activity or the passage of the tick-borne pathogens acquired during blood feeding. Most of the 418 putatively identified transcripts expressed in this library appear to be novel. Similarly, the remaining unidentified transcripts also lack significant similarities to known tick or insect proteins. This report makes all available for inspection and further study.

Solvents and organic compounds
Water was 18 MΩ quality produced on site using a MilliQ water purification system (Millipore, Bedford, MA, USA). Organic compounds were obtained from Sigma Chemical Corporation (St. Louis, MO, USA) or as stated.

Ticks
Dermacentor variabilis was colonised and maintained as described previously [84]. Two groups of virgin female ticks were used to create the cDNA midgut library. Briefly, group 1 comprised blood-fed ticks that had fed 6-day on New Zealand white rabbits (Oryctolagus cunniculus); group 2 comprised ticks that had fed 2-day on rabbits, along with unfed females. All use of animals for this research was done in accordance with protocols approved by the Old Dominion University Institutional Animal Care and Use Committee (IACUC). The approved protocols are on file in the Old Dominion University Animal Care Facility Office.

Tissue collection and cDNA library construction
Blood-fed virgin female ticks were detached from their rabbit hosts, surface-sterilised with 3% H 2 O 2 and 70% ethanol and dissected to expose the midguts. For group 1, samples of midgut tissues were excised from five females, washed 1 × with phosphate-buffered saline (PBS, pH 7.2) and immersed in RNAlater (Ambion, Austin, TX) at 4°C until needed. For group 2, sample midgut tissues were excised from ten 2-day-fed females and ten unfed females, washed as described above, combined and immersed in RNAlater. The Micro-Fast Track mRNA isolation kit (Invitrogen, San Diego, CA, USA) was used to isolate mRNA in accordance with the manufacturer's instructions with some modification [78]. Briefly, the SMART cDNA library construction kit (Clontech, Palo Alto, CA, USA) was used to create the PCR-based cDNA library. A 100 ng of mRNA was reverse transcribed using the SMART PowerScript™ reverse transcriptase and CDS III/3' PCR primer (Clontech) for 1 h at 42°C. Second strand synthesis was done with a PCR-based protocol using the SMART 5' PCR primer (Clontech) as the sense primer and CDSIII/3' PCR primer as the antisense primer. These primers create SfiI A and B sites as the ends of the nascent cDNA. Doublestranded (ds) cDNA synthesis was carried out using a Perkin-Elmer 9700 Thermal cycler (Perkin Elmer Corp., Foster City, CA, USA) using the Advantage 2 taq-Polymerase (Clontech). PCR conditions were as follows: 95°C for 1 min, then 8 cycles at 95°C for 10 s and 68°C for 6 min, allowed to cool (4°C) and a 3 μl aliquot removed and stored. PCR amplification was repeated and additional aliquots removed after every 2 cycles until a total of 18 cycles had elapsed. The aliquots from each group of cycles were run on an agarose gel with Ethidium Bromide (EtBr) and the optimum number of cycles that would avoid over amplification of the most abundant cDNAs was determined. The double-stranded cDNA was treated with peptidase K (0.8 μg/μl) and washed (H 2 O) 3 × using 100 mol wt cut off (MWCO) Amicon filters (Millipore). After cleaning, the double-stranded cDNA was digested with SfiI enzyme at 50°C and the cDNA fragments were fractionated using the Chroma spin™ columns provided (Clontech). Fractions were separated into three different sizes (large, medium and small), concentrated, washed (H 2 O), filtered (100 kDa Amicon filters), concentrated and ligated into a λ-TriplEx-2 vector (Clontech). The ligation reaction product was packed using the Gigapack Gold III kit (Stratagene, Cedar Creek, TN, USA) according to the manufacturer's instructions. The resultant library was plated by infecting log-phase XL-1 blue cells (Clontech). The amount of recombinants was determined by PCR using the vector primers flanking the inserted cDNA and then visualised on agarose gels (ethidium bromide).

Sequencing the D. variabilis midgut library
The cDNA libraries from the two groups were plated (200 plaques/150 mm plate). Plaques were picked at random and transferred to the wells of a 96-well propylene plate containing 75 μl/well. Bacteriophage (4 μl), forward and reverse primers, sequencing reactions and cleanup were done as described previously [78]. Cleaned PCR products were used as a template for cycle-sequencing reactions using BigDye Terminator v3.1 cycle sequencing kit (Applied Biosystems, Foster City, CA). Sequencing reactions were cleaned using a multiscreen 96-well plate cleaning system (Millipore, Billerica, MA). Dried samples were resuspended with 25 μl of deionised, ultrapure, formamide. Samples were directly sequenced on an ABI 96 capillary DNA sequencer (Applied Biosystems, Foster City, CA) or stored at -80°C.

Bioinformatics analysis
A detailed description of the bioinformatic treatment of the data appears in Valenzuela et al. [85]. Data manipulation was preformed using a set of customised executable programs written in Visual Basics by José M.C. Ribeiro at the National Institutes of Health. Primer and vector sequences were removed from the raw sequences and the resultant (cleaned) sequences were compared against the NR protein database using an executables program obtained at the NCBI FTP site [91]. Related sequences were grouped into clusters and aligned using CAP3 sequence assembly program [92]. Using the appropriate BLAST algorithm (BLASTX, BLASTN or RPS-BLAST), individual concensus sequences and singletons were compared to the NR protein database of the NCBI, the GO fasta subset [93], CDD of NCBI [20] containing the KOG [94], Pfam [95] and SMART [96] protein motif databases [18] and to custom-downloaded databases containing the ACARI (a subset containing mite and tick sequences), mitochondrial/plastid and rRNA nucleotide sequences available at the NCBI. We submitted all translated sequences (starting with a Met) to the Signal P server [97] to detect signal peptides indicative of secretion. The threeframe translation of each dataset was used to determine open reading frames (ORF). Only ORF that started with a methionine and were longer than 40 amino acid (AA) residues were submitted to the SignalP server. The grouped and assembled sequences, BLAST results and signal peptide results were combined in an Excel spreadsheet and manually verified and annotated. A stand alone file which the user should download and extract is found at: http:// exon.niaid.nih.gov/transcriptome/D_variabilis_midgut/ DVMG.tar.gz. Additionally, a hyperlinked excel file can be obtained from: http://exon.niaid.nih.gov/transcriptome/ D_variabilis_midgut/DVMG-web.xls

Phylogenetic analysis
For phylogenetic analysis of transcripts of interest, the consensus sequence was translated into the appropriate open-reading frame using EditSeq software (DNAStar). Related protein sequences were downloaded from NCBI and aligned using ClustalX [98]. The resulting alignment was manually refined and trimmed using BioEdit sequence-editing software [99]. Alignments were then submitted to ProtTest version 1.2.6 [100] to determine the best-fit model protein substitution for each particular alignment. Phylogenetic analysis was conducted on protein alignments using Tree Puzzle version 5.2 [101] incorporating the predicted model of evolution as defined by ProtTest. Tree Puzzle constructs phylogenetic trees by maximum likelihood using quartet puzzling, automati-cally estimating internal branch node support (1000 bootstrap replications) [102]. Trees were visualised and annotated using Mega 4.0 [103]. The names of the sequences in the alignments and phylograms were abbreviated with the species initials and GenBank accession number; for the transcripts from the cDNA libraries, the transcript number was added.

Supplemental material
To save space and simplify reading, many of the supporting figures are located in the form of supplemental materials hyperlinked throughout the paper either to the NCBI page [104] where this and other transcriptomes are located or to the publisher's archives associated with this paper. Readers may access these materials by clicking on the hyperlinked files.

Protein identification
Blood-fed female ticks were detached, surface washed with 70% ethanol: 3% H 2 O 2 to remove contaminants. The midguts were removed, washed in PBS buffer and homogenised in cold (4°C) in lysis buffer containing 20 mM Tris-HCL, 137 mM NaCl, 2 mM EDTA, 0.1% Triton-X 100 and 10% glycerol [105], supplemented with 0.1 -0.2 mM PMSF (Sigma, St. Louis, MO, USA) and a 200-fold dilution of peptidase inhibitor cocktail (Sigma). The extract (N = 25) was sonicated, centrifuged at 14,000 × g, and then frozen (-20°C) until needed. Bradford protein assays were performed as described by the manufacturer (BioRAD, Richmond, CA) using immunoglobulin G as the standard. Samples (~40 μg per lane) of the midgut protein extract were electrophoresed using NuPage 4 -12% 1 mm thick gradient gels under reducing conditions in accordance with the manufacturer's instructions (Invitrogen). Relative mol wts were estimated using pre-stained SeeBlue™ and unstained Mark 12™ mol wt markers (Invitrogen). For amino-terminal sequencing of the midgut proteins, the proteins were electro-blotted to PVDF blot paper in a Xcell II Mini-Cell with transfer buffer (Invitrogen) and the membrane stained with 0.025% Coomassie Blue (R) in the absence of acetic acid. Stained bands were cut from the blot membrane and subjected to Edman degradation in a Procise sequencer (Perkin Elmer Corp.). The resultant AA sequences were searched against the most likely protein translations of each cDNA sequence obtained in the mass sequencing project, as described previously [78]. Identifications were also done by tryptic digestion/mass fingerprinting of selected gel slices excised from the protein gels at the University of Virginia's Keck Biomolecular Research Facility as described previously [3,80], and at the Proteomics Facility, Research Technology Branch, National Institute of Allergy and Infectious Diseases. The sensitivity of detection would detect proteins or peptides even when present in concentrations as low as 1% of the sample.