- Research article
- Open Access
The small heat shock protein (sHSP) genes in the silkworm, Bombyx mori, and comparative analysis with other insect sHSP genes
© Li et al; licensee BioMed Central Ltd. 2009
Received: 20 May 2009
Accepted: 28 August 2009
Published: 28 August 2009
Small heat shock proteins (sHSPs) are products of heat shock response and of other stress responses, and ubiquitous in all three domains of life, archaea, bacteria, and eukarya. They mainly function as molecular chaperones to protect proteins from being denatured in extreme conditions. Study on insect sHSPs could provide some insights into evolution of insects that have adapted to diverse niches in the world.
Taking advantage of the newly assembled genome sequence, we performed a genome-wide analysis of the candidate sHSP genes in the silkworm, Bombyx mori. Based on known silkworm sHSP sequences, we identified 16 silkworm sHSP genes. Most of them are distributed on two silkworm chromosomes 5 and 27, respectively. 15 of 16 silkworm sHSPs have expression evidence. The comparative analysis of insect sHSPs from B. mori, Drosophila melanogaster, Apis mellifera, Tribolium castaneum, and Anopheles gambiae revealed that there is only one orthologous cluster whereas remaining clusters are species-specific on the phylogenetic tree. This suggested that most of sHSPs might have diverged in function across insects investigated. In addition, the data presented in this study also revealed that sHSPs in the insect orthologous cluster are highly conserved in both sequence and expression pattern. In sum, insect sHSPs show a completely different evolutionary pattern from that found in vertebrate sHSPs.
B. mori has the largest number of insect sHSP genes characterized to date, including 16 genes. The inference that most species-specific sHSPs might have diverged in function across insects investigated will help us understand the adaptability of these insects to diverse environments.
It was in Drosophila that researchers observed the phenomenon of heat shock response (HSR) at the first time . Then these proteins highly expressed in thermal stress were defined as heat shock proteins (HSPs). Previous studies suggest that the small heat shock proteins (sHSPs) are abundant and ubiquitous in almost all organisms, from bacteria to algae with single cell to the higher organisms including human [2–5]. HSPs can be divided into five families, including HSP100, HSP90, HSP70, HSP60, and sHSP. This classification is mainly based on the molecular weight as well as the homologous relationship of HSPs. All of these families are conserved, except for sHSP family that is more diverse than other four. However, there are some common characteristics in the function and structure of sHSP. The molecular weights of sHSPs range from 12 kDa to 42 kDa, usually bellow 30 kDa [2, 4]. The sHSPs have an α-crystalling domain comprising about 100 amino acid residues, which is the conserved structure of all sHSP sequences [6–8]. There is a conserved β-sheet sandwich in sHSP secondary structure, and it is these β-sheet structures that help several subunits of sHSP to form a large oligomer [2, 9, 10]. This stable multimeric structure formed by sHSPs has the function of molecular chaperone, which binds to the proteins and prevents them from thermal denaturation [10–12]. The low molecular weight, the conserved secondary structure, and protein domain are principal features used to identify a protein belonging to sHSP family.
In addition to functioning as molecular chaperones to protect proteins from being denatured in high temperature stress [10, 13], sHSPs can also develop the protection function in the conditions of other stresses, such as cold, drought, oxidation, hypertonic stress, UV, and heavy metals [4, 14], even high population density of organisms . The HSPs including sHSPs are playing the part of chaperone function not only in stress conditions, but also in normal development . Although the sHSP family has relatively conserved function of molecular chaperone and the C-terminal of these proteins harbors the conserved α-crystalling domain, the N-terminal sequences of these proteins are variable. This indicates that the conserved C-terminal sequence is a significant part for sustaining the chaperone and other functions of sHSP in cells or organisms whereas the diverse N-terminal sequences may be associated with the diverse expressions, functions, and evolutionary patterns among sHSPs.
There have been numerous studies on HSPs in bacteria, algae, plant, amphibians, birds, and mammalian, especially in the model organisms of Arabidopsis thaliana, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, zebra fish, Mus musculus[3–5]. Although the heat shock response was fist discovered in insect , the study of HSP in insects, especially for sHSP, is not as extensive and penetrating as in other organisms. sHSPs primarily have chaperone activity and reflect the response machine of organisms to some extreme stresses existing in environment. Insects are one of the most successful organisms in the world and have a strong ability to adapt to various habitats. So the study of insect sHSP is necessary.
In this study, we first identified the sHSP genes of Bombyx mori based on the new assembly of the silkworm genome sequence http://silkworm.swu.edu.cn/silkdb/. Then we performed comparative analyses with the sHSPs from other four insects whose complete genome sequences are available. It was found that there is an orthologous cluster including five sHSP genes that come from each of five insects. This group of genes is so conserved in sequence among insects, which is in sharp contrast to the other sHSP genes that are species-specific and show the evolutionary pattern of lineage-specific expansion. In addition, the expression patterns of the silkworm sHSPs were investigated by available microarray data. Our data provide some new insights into evolution and functions of the insect sHSPs.
sHSP genes in silkworm and other insects
The sHSP genes in B. mori
Scaffold and Interval
Predicted molecular weight (Da)
Sakano et al.2006
Sakano et al.2006
Sakano et al.2006
Li et al.2005
Sakano et al.2006
Liu et al.2008
Sakano et al.2006
B. mori has 28 chromosome pairs. It can be known from Table 1 that the genes encoding sHSPs were distributed on at least four chromosomes 27, 5, 19, and 13. Because the scaffolds nscaf2803 and scaffold2784 could not be located on the chromosomes in current version of the silkworm genome sequence, the locations of Bm21.6 (in nscaf2803) and Bm20.1 (in scaffold2784) were not determined. It is clear that the distribution of the silkworm sHSP genes in the genome is not homogeneous. There are six sHSP genes located on the silkworm chromosome 27, five genes on chromosome 5, two genes on chromosome 19, and only one gene on chromosome 13. In addition, we found that genes distributed on the chromosomes 27 and 5 have no intron. One gene, Bm22.6 distributed on chromosome 19, contains one intron (the intron length is 2982 bp), and another one, Bm21.4 distributed on chromosome 13, contains two introns (the lengths are 5263 bp and 620 bp, respectively). Compared with the full-length (400~750 bp) of most of the silkworm sHSP genes, these two genes containing introns are relatively too long, especially for Bm21.4. In the previous report , the complete gene sequence of Bm21.4 could not be amplified through PCR method using silkworm genomic DNA as template. Probably, this is due to existence of a relatively big intron. Bm22.6, Bm21.4, and Bm42.3 are different from the other silkworm sHSP genes in chromosome location and the existence of intron. It can be seen from Table 1 that Bm20.8, Bm20.4, Bm19.1, and Bm19.9 are tandem arranged on the middle region of chromosome 27 and there is no any other gene interrupting this genomic region. Bm 23.8 is located on the near end of chromosome 27. However, only two of five sHSP genes on chromosome 5 are tightly tandem arranged (Table 1 and Additional file 1).
The sHSP genes in other four insects
Predicted molecular weight (Da)
Silkworm has the largest number of sHSP genes (16 genes) whereas An. gambiae has the least number of sHSP genes (7 genes) among the insects investigated. With the information of chromosome location and intron number, we can roughly divide the sHSP genes into two types for each of the species. One is that the genes clustered on the same chromosome (two chromosomes for silkworm) tend to have no intron and the other is that the genes (1 to 3 genes) dispersed on chromosomes tend to have intron.
We also performed homology search in the genome of S. cerevisia and found two genes that have high identity with silkworm sHSP genes. One is Scer23.9, located on the chromosome 2. This gene has been reported previously and its NCBI accession number is NP_009628.1. We used it as the outgroup in the phylogenetic analyses.
Phylogenetic analysis of insect sHSP genes
Figure 2 shows that there are two types of clusters on the phylogenetic tree. One type is an orthologous cluster with a very high supporting value measured by the posterior probability, which includes five members that come from each of five insects, respectively. These genes all have at least two introns and dispersed in genomes without any linkage relationships to other sHSP genes. The sHSP genes of D. melanogaster (Dmel20.8) and An. gambiae (Agam20.9) are located on the chromosome X, which is the sex chromosome. The branching pattern of the orthologous cluster shows that Dmel20.8 and Agam20.9 are closer in five orthologous genes and Amel25.6 and Tcas21.8b are closer. Surprisingly, Bm21.4 did not cluster closely to Diptera but was placed on the basal of the cluster, which is not consistent with the result of a recent study on insect molecular systematics . This may imply that Bm21.4 might have experienced a specific evolutionary process.
The other type on the phylogenetic tree is species-specific clusters as a result of lineage-specific expansion. Silkworm-specific cluster includes 12 sHSP genes but has a relative low support value. Most of these genes are located on two chromosomes 5 and 27, however, Bm27.4 and Bm26.6 located on chromosome 5 are not included in this cluster. Bm42.3 is also contained in this cluster.
The posterior probabilities of the species-specific clusters in other four insects are higher (Figure 2). In Ap. mellifera, the species-specific cluster contains 7 sHSP genes and all these genes are distributed on chromosome 2. Additionally, 6 of these genes have no intron except Amel21.3 contains one intron. It is interesting that Amel22.0 located on chromosome 2 and with three introns is not the member of this cluster. In D. melanogaster, sHSP genes distributed on the left arm of chromosome 3 are all included in the species-specific cluster. The gene of Dmel24.5 located on chromosome 2 is also in this cluster. All these genes have no intron. Most of members of the species-specific cluster of T. castaneum sHSP are located on chromosome 8 and only Tcas22.2 is on chromosome 3. They are all single exon genes. Three sHSP genes on the same chromosome of An. gambiae formed a cluster and they all have no intron. In addition, there are other sHSP specific genes in An. gambiae, including Agam21.7, Agam21.6, and Agam23.5b. These three genes have two or three introns and are also located on chromosome 2. All tandem arranged genes of each species except An. gambiae are included in the species-specific cluster (Table 1, Table 2 and Figure 2).
Most strikingly, most members in each of species-specific clusters are usually distributed on the same chromosome in a tandem manner. This gene expansion may be the result of gene duplication events created by unequal crossing over.
The orthologous sHSP genes in insects
We performed blast searching Genbank with these orthologous sHSP sequences to look for orthologous sHSPs in other insects or distant species. We did find that many other insects have this orthologous gene, such as Acyrthosiphon pisum (Accession no. XP_001949402), Aedes aegypti (XP_001657982), Culex quinquefasciatus (XM_001870731), Heliconius erato (ABS57447), Locusta migratoria (ABC84493), and Nasonia vitripennis (XP_001607669). Furthermore, an arthropods of Ixodes scapularis (EEC06453) belonging to Arachnoidea and four nematoda organisms of Caenorhabditis briggsae (XP_001676833), C. elegans (NP_001024374), Brugia malayi (U48407) and Dirofilaria immitis (AAB08736) also contain the orthologous sHSP genes which are slightly divergent from the insect orthologs. Compared with the five orthologous sHSP genes in Figure 2, the homologous genes mentioned above have not only high identity but also a conserved N-terminal, which is the principal structure characteristic of the genes in the orthologous cluster (Additional file 3). So, this kind of orthologous genes exists not only in insects but also in other invertebrates.
To confirm whether the orthologous group genes exist in vertebrate, we reconstructed a larger phylogenetic tree including sHSP genes from above five insects, nematode, amphioxus, mouse and human (Additional file 4). The sequences of sHSP genes in nematode, mouse and human came from previous studies [5, 21, 22]. 14 amphioxus sHSP genes were obtained by searching the genome of Branchiostoma floridae  using blast method. The phylogenetic analysis results indicated that, as expectation, a nematode sHSP gene Ce25 was included in the highly supported orthologous cluster but the human and mouse sHSP genes were not in it. However, the HsapHspB11 from Human and MmusHSPB11 from mouse as well as two sHSP genes from amphioxus formed a cluster although the support value is low. Furthermore, this cluster seems to be close to the orthologous group (Additional file 4). Therefore, it appears that a kind of highly conserved sHSP genes may exist even in vertebrates. In addition, we observed that there are many orthologous sHSP clusters between human and mouse, which is consistent with previous studies [21, 22].
The species specific sHSP genes in insects, especially in the silkworm
Our study revealed that most insect sHSP genes are species-specific (Figure 2). The silkworm contains the most number of the species-specific sHSPs. They all have a conserved α-crystalling domain and a diversified N-terminal region. Whether there are divergent expression patterns in these paralogous genes is worthy to be detected for this domesticated insect, B. mori.
We searched for EST evidences of sHSP genes through SilkDB . 14 silkworm sHSP genes have complete EST sequences except Bm21.6 and Bm42.3. But Bm21.6 had been cloned in previous studies, as well as the genes of Bm19.9 [17, 18], Bm23.8, Bm20.8, Bm20.4, Bm21.4, and Bm20.1 , Bm24.2 , Bm19.1, Bm15.7, Bm 22.6, Bm27.4, Bm20.2, and Bm19.5 (not published). So, 15 silkworm sHSP genes are certainly transcribed. In fact, there is no EST sequence associated with Bm42.3. Several possible reasons may explain the absence of EST evidence for Bm42.3. One is that this candidate silkworm sHSP gene is not expressed in usual conditions or its expression is too weak to be detected. Another is that it might have lost its regulatory elements. All of these should be confirmed in future.
In this study, we first identified 16 silkworm sHSP genes based on the new assembly of the B. mori genome sequence , which is the largest number of the sHSPs of five insects in different orders that whole genome sequences are available. Previous study based on six silkworm sHSP genes suggested that the sHSP genes in the silkworm may be classified into two groups . Similarly, the comparative analysis of sHSPs in five insects revealed that there are two types of clusters of insect sHSPs: one is orthologous and the other is species-specific. Interestingly, there is one orthologous cluster that includes one sHSP from each insect whereas most insect sHSPs are species-specific (Figure 2). These results suggested that most insect sHSPs might have experienced lineage-specific expansion and diverged in function at least amongst insect orders. Nevertheless, a few insect sHSPs such as those in orthologous cluster are highly conserved in whole sequence as well as in gene structure, suggesting that they may also have highly conserved function. The phylogenetic relation of the orthologous cluster may be interpreted as the speciation history.
Most members of species-specific cluster are tandem arranged genes in each insect and there is no orthologous relationship between tandem genes of different insects. This case may occur if a primitive tandem set with several genes existed in the ancient of the five insects, subsequently, frequent and general gene conversion events homogenize the tandem sHSP genes in each insect after the speciation, finally the originally orthologous sHSP genes became species-specific. So we estimated the gene conversion events of sHSP genes in each insect with GeneConv program http://www.math.wustl.edu/~sawyer/geneconv/. Surprisingly, although the P values are below 0.01, the predicted gene conversion nucleotide residues are no longer than 40 bp in our tests (most are below 25 bp) except a gene pair in the silkworm of Bm20.8 and Bm 20.4 (P value, 0.001; length, 128 bp). These results imply that gene conversion is not the major mechanism explaining the topology in Figure 2. Therefore, our observations do not support the assumption above. Members of species-specific cluster or tandem arranged genes might be the result of independent gene expansion occurred during evolution of each insect.
The gene expansion process may associate with gene duplication and loss events, which are known as a birth-and-death model. This model was successfully used to interpret some evolutionary process of most gene families including HSP70 and cytochrome P450 [27, 28]. If this is the case, Figure 2 suggests that some gene duplication events of sHSPs occurred before the radiation of insects, and that one or two copies experienced lineage-specific expansions through successive gene duplications after the radiation of insects.
The tandem arranged pattern of sHSP genes is not exclusive in insects. For example, sHSP16 genes in C. elegans and C. briggsae also show similar pattern . The tandem repeats of sHSP genes may facilitate organisms to rapidly respond to changing environmental conditions because of regulation reason. All the five insects have independently developed this strategy for sHSP genes, which is similar to the convergent duplication of the proneural genes in insects . However, the 10 sHSP genes in human are separately distributed on eight chromosomes . The different arranged forms of sHSP genes may reflect different evolutionary processes that organisms experienced. Tandem sHSP genes may be a better way for insects to regulate gene expressions in diverse environments.
It is known that the sHSPs are members of HSP family with function of molecular chaperone. They are ubiquitous in all organisms and extremely conserved in the sequence structure of α-crystalling domain resided in C-terminal. The conserved C-terminal region might be the result of strongly functional constraint of sHSPs as a molecular chaperone. sHSPs bind to other cellular proteins in thermal and other extremely devastating stresses, and protect them from denaturation. They also have functions in protein folding and transportation, the embryo development and immunization mechanism of organisms. The conservative degrees of sHSP genes are heterogeneous in different protein regions. In general, the N-terminal coding sequences are more variable than C-terminal with the α-crystalling domain. However, the sHSPs in the orthologous cluster showed high conservation along whole sequence. The orthologous sHSP gene (Bm21.4) in silkworm was cloned and found to be not induced by thermic stress (45°C), and it was expressed constitutively in normal conditions (room temperature) in fat body and other tissues of silkworm . The microarray data also revealed the similar expression patterns (the probe number is sw01265). So Bm21.4 is special in sequence and expression compared with other silkworm sHSP genes . These observations suggest that insect orthologous sHSPs may not be associated with response of insects to environmental stresses. In contrast, they may be involved in basically metabolic processes in insects.
One previous study based on the limited number of sHSP sequences suggested that the phylogenetic relationship of sHSP genes in insects is quite different from that of other species or taxonomical groups . Mammals have at least ten sHSP subfamilies and they also have orthologous genes in zebrafish . The identified sHSP genes in amphibians are also orthologous to those of mammals . In general, there are multiple orthologous sHSP clusters in vertebrate and angiosperm sHSPs also have similar pattern [4, 32]. However, insect sHSP genes principally show one orthologous cluster that is composed of each sHSP from each species investigated, and most of the genes are species-specific (Figure 2). Thus, insect sHSPs display completely different evolutionary pattern from that of vertebrates or plants.
To determine whether the evolutionary pattern observed in five insects is universal for other arthropods and nematode, we searched the GenBank for the orthologous sHSPs in corresponding species. Indeed, we found orthologous sHSP genes in many other arthropods and nematode (Additional file 3). Most of these species are insects, such as L. migratoria, He. erato , Ac. pisum, and Ae. aegypti. These insects cover the orders Lepidoptera, Hymenoptera, Diptera, Hemiptera, Coleoptera, and Orthoptera. This ubiquitous existence in insects suggests that all of the species of insecta may possess one copy of this conserved gene in their genomes. There is a species of Arachnida, I. scapularis, that contains this orthologous gene. This gene is also detected within each of nine nematode species . A species of chordate, Branchiostoma lanceolatum, also contains this orthologous sHSP gene named B1Hsp24.1 (GenBank accession number: AJ616737) with relatively lower identity . Insecta and Arachnida belong to the phylum Arthropoda. Furthermore, Arthopods, Branchiostoma, and phylum Nematoda are all invertebrates. So, these orthologous sHSP genes do exist in Arthropods and Nematode and probably in all invertebrates.
That insects harbor orthologous sHSP genes is interesting. To know how these gens are related to the vertebrate sHSPs, we performed the phylogenetic analysis on the sHSPs from five insects, nematode, amphioxus, mouse and human. Although no highly supported orthologous cluster was found on the phylogenetic tree, it seems that vertebrates also have the highly conserved sHSPs that are close to insect orthologs. Therefore, it is important to understand functions of these conserved sHSPs of different organisms in future.
The orthologous sHSP genes have not only the conserved sequences but also the conserved gene structure across insect orders probably and the sequences of α-crystalling domains in these genes are more conserved than that in species-specific genes, all of which is the result of strongly purifying selection during evolution. P27, another orthologous gene of Bm21.4 in Di. immitis, is also constitutively expressed in male and female adult worms and developmental phase such as L3–L4 molt and is located in hypodermal tissues. Additionally, it is not up-regulated by heat shock at 43°C . In C. elegans, Ce25 is also constitutively expressed in normal conditions and this protein is principally located in body wall muscle specially bonding to vinculin and α-actinin . However, the orthologous gene in migratory locust, hsp20.6, can regulate its expression associated with the population density, for example, high density corresponding to an increased expression . We infer that these orthologous sHSP genes may be constitutively expressed in organisms and may not be involved in the heat shock response. It is likely that they are house-keeping genes and important in the development, adaptability and metabolism of organisms.
Another important feature of insect sHSPs is that most of them are species-specific in five insects investigated. This suggested that functions of most sHSPs might have diverged among the insects, reflecting that the sHSPs might have contributed to adaptability of insects to different niches. Silkworm has the largest cluster of species-specific sHSPs which includes 12 genes although the cluster has a relatively low supporting value measured by posterior probability. 12 silkworm species-specific sHSPgenes diverged in sequences especially in N-terminal region (Figure 1). There are several previous studies focused on these proteins [17–19, 36–38]. Silkworm sHSP genes Bm20.4, Bm20.8, Bm19.9, Bm20.1, Bm24.2, Bm23.8, and Bm19.5 have increased expression by heat shock stress [17–19, 38]. It is the sHSP genes belonging to species-specific cluster that principally participate in heat shock response of silkworm and other insects. However, these genes are also expressed in usual conditions without extreme stress and have distinct expression levels in different tissues of silkworm (Figure 4). The expression of Bm19.9 is significantly high in testis and ovary , and Bm20.1 is highly expressed in testis of the fifth instar . There are other sHSP genes having high expression intensities in gonad through the microarray data (Figure 4). Silkworm sHSP genes highly expressed in gonad may play an important role in the development of germocyte. Bm19.1, Bm15.7, and Bm23.8 are increasedly expressed in midgut. Furthermore, Bm22.6, which does not belong to the species specific cluster, is also highly expressed in midgut (Figure 4). Additionally, Bm22.6 is one of the 11 genes significantly up-regulated in midgut following the infection of BmDNV-Z, a densonucleosis virus . Bm22.6 and Bm19.1 are also remarkably expressed in integument (Figure 4). Integument and midgut are tissues with immune function. Previous studies suggest that HSPs may participate in the innate immune responses of silkworm . So the silkworm sHSP genes highly expressed in midgut or integument may have functions in immune defense mechanism.
There are some changes in cellular physiology before and after the heat stress. Bm20.1 principally located in nucleus and Bm20.8 in cytoplasm, are all transferred to the membrane after heat shock, and then recovered to the previous subcellular localization in normal conditions. This implies that sHSP have functions in the membrane structure and metabolism in extremely conditions [41, 42]. Silkworm sHSP genes also have been studied in embryonic development of diapause and non-diapause eggs , silkworm parthenogenesis , and different silkworm breeds of bivoltine and multivoltine . The studies in heat stress induced pattern, expression diversity in tissues, and other functions without chaperone of silkworm sHSP genes suggest that there are divergences in the biological functions among these genes. These species-specific sHSP genes may resist harmful stimulus for organisms and participate in the reproduction, development, and the normal metabolism activities. It is believed that the diversity and divergence of sHSP genes might have facilitated the insects adapting to various environments.
The data presented in this study revealed that the majority of insect sHSP genes in each species are located on one chromosome except for that most silkworm sHSP genes are located on two chromosomes 5 and 27. It is possible that the distribution of most silkworm sHSP genes on chromosomes 5 and 27 might be the result of split of an ancient chromosome. However, there is opposed evidence against this scenario, which is that silkworm chromosomes 5 and 28 correspond to one chromosome in He. erato and silkworm chromosomes 23 and 27 correspond to another one . So, the expanding process of sHSP genes in silkworm is complicated. The silkworm has the most number of sHSP genes, and An. gambiae has the least. Whether there is relationship between the number of the sHSP genes and the resistance to thermal or other stresses is unknown. The multivoltine silkworms are more resistant than bivoltine in thermal stress, and the expressions of some sHSP genes in multivoltine breeds are lower compared with the bivoltine breeds after heat shock at 45°C . The gregarious locust expresses more sHSP genes than solitary locust due to different population density, and the former have a smaller body size and a weaker fecundity . Therefore, the sensitivity to heat and other stresses may influence the development and reproduction of various voltinism breeds in silkworm.
Based on known silkworm sHSP sequences and the newly assembled genome sequence, we identified 16 silkworm sHSP genes. 15 of 16 silkworm sHSPs have expression evidence. The comparative analysis with other insect sHSPs revealed that there is only one orthologous cluster whereas remaining clusters are species-specific. Our data demonstrated that the evolutionary pattern of insect sHSPs which is different from that found in vertebrates and will provide some new insight into evolution of insect sHSPs. It is believed that studies on the evolution, function and mechanism of stress response genes in insects will help us understand the adaptability of insects to diverse environments.
Identification of insect sHSP genes
We first retrieved 6 known sHSP sequences of B. mori from Genbank  and then used these sequences as queries to search the new assembly of the silkworm genome sequence in SilkDB http://silkworm.swu.edu.cn/silkdb for a complete list of the silkworm sHSPs. The E value for evaluating all sequences in homology search is 10-4. Finally, we obtained 16 sequences as candidate genes for the silkworm sHSPs. The other four insect annotated gene and protein sequences were downloaded from NCBI website http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/. The four insects are D. melanogaster, Ap. mellifera, T. castaneum, and An. gambiae. We used above 16 sHSP sequences of B. mori as queries to perform the same homology search for other insect sHSPs as above.
One sHSP gene sequences of S. cerevisiae was used as the outgroup. This sequence was retrieved from Genbank (Accession no. NP_009628).
The secondary structure and structural domains and chromosome locations of the insect sHSPs
The information of protein secondary structure and domain has advantage for helping researchers to understand the function of these proteins. So the structure information of B. mori candidate sHSP genes was predicted by PredictProtein http://www.predictprotein.org/, one online service tool. The prediction of protein domain was performed on InterProScan online service http://www.ebi.ac.uk/Tools/InterProScan/.
The location information of B. mori sHSP genes on the chromosomes was obtained by SilkMap online tool http://silkworm.swu.edu.cn/silksoft/silkmap.html. The location information of the other four insect sHSP genes was determined by Map View tool http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/mapview/ at NCBI website.
The amino acid sequences of sHSP genes of five insects were aligned by three methods, clustal X v.1.8, clustal W v.1.83 , and muscle v.3.6 . The resulting alignments were almost identical and one of them was selected for further analyses. The phylogenetic tree for the insect sHSPs was first reconstructed by Neighbor-Joining (NJ) method in which distance was estimated by JTT amino acid matrix implemented in the program MEGA 4 . The pairwise deletion option was used in the NJ tree reconstruction and the accuracy of the tree topology was assessed by bootstrap analysis with 1,000 resampling replicates.
Using the amino acid sequences of the conserved α-crystalling domain with 100 residues, we also reconstructed the phylogenetic relationship of the insect sHSP genes by the program MrBayes v.3.1.2 . MrBayes is a program of reconstructing phylogenetic relationships based on Bayesian and maximum likelihood methods. This program simulates the posterior distribution of the phylogenetic trees through the method of Metropolis-coupled Markov Chain Monte Carlo . WAG model was demonstrated to be the best model used in the MrBayes program to reconstruct the phylogenetic tree for the amino acid sequences of insect sHSPs. After MrBayes program with WAG model run 6500000 generations, the value of average standard deviation of split frequencies became stable below 0.01 and finally reached to 0.007103 at the end of the running. So, the early 3500000 generations data were seen as the burnin, which were deleted in the analysis of the results. All the trees are rooted by the sHSP gene sequence of S. cerevisiae, scer23.9.
Expression information based on microarray database
B. mori microarray database http://silkworm.swu.edu.cn/microarray/ is composed of expression data for 22987 probes of 9 silkworm tissues on day 3 of the fifth instar in silkworm . We used blastn search to obtain expression information of each silkworm sHSP gene in several tissues at normal or some stress conditions. We also searched the EST data for the silkworm sHSP genes in SilkDB to confirm whether these genes identified from the genome search approach are expressed in the organism or not http://silkworm.swu.edu.cn/silkdb.
We thank one anonymous reviewer for constructive comments that improved the manuscript. This study was supported by the Hi-Tech Research and Development (863) Program of China (2006AA10A117), a grant from National Science Foundation of China (No. 30671587), and the Programme of Introducing Talents of Discipline to Universities (B07045).
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