A genome-wide identification and analysis of the basic helix-loop-helix transcription factors in the ponerine ant, Harpegnathos saltator

  • Ake Liu1,

    Affiliated with

    • Yong Wang2Email author,

      Affiliated with

      • Chunwang Dang1,

        Affiliated with

        • Debao Zhang1,

          Affiliated with

          • Huifang Song1,

            Affiliated with

            • Qin Yao1 and

              Affiliated with

              • Keping Chen1

                Affiliated with

                BMC Evolutionary Biology201212:165

                DOI: 10.1186/1471-2148-12-165

                Received: 11 May 2012

                Accepted: 20 August 2012

                Published: 31 August 2012

                Abstract

                Background

                The basic helix-loop-helix (bHLH) transcription factors and their homologs form a superfamily that plays essential roles in transcriptional networks of multiple developmental processes. bHLH family members have been identified in over 20 organisms, including fruit fly, zebrafish, human and mouse.

                Result

                In this study, we conducted a genome-wide survey for bHLH sequences, and identified 57 bHLH sequences encoded in complete genome sequence of the ponerine ant, Harpegnathos saltator. Phylogenetic analysis of the bHLH domain sequences classified these genes into 38 bHLH families with 23, 14, 10, 1, 8 and 1 members in group A, B, C, D, E and F, respectively. The number of PabHLHs (ponerine ant bHLHs) with introns is higher than many other insect species, and they are found to have introns with average lengths only inferior to those of pea aphid. In addition, two H. saltator bHLHs named PaCrp1 and PaSide locate on two separate contigs in the genome.

                Conclusions

                A putative full set of PabHLH genes is comparable with other insect species and genes encoding Oligo, MyoRb and Figα were not found in genomes of all insect species of which bHLH family members have been identified. Moreover, in-family phylogenetic analyses indicate that the PabHLH genes are more closely related with Apis mellifera than others. The present study will serve as a solid foundation for further investigations into the structure and function of bHLH proteins in the regulation of H. saltator development.

                Keywords

                Basic helix-loop-helix Transcription factor Harpegnathos saltator Phylogenetic analysis Orthologous family Blast search

                Background

                Since the first basic helix-loop-helix (bHLH) motif with DNA-binding and dimerization capabilities was reported [1], numerous bHLH proteins have been found to be intimately involved in the regulation of a wide range of developmental processes, including neurogenesis, myogenesis, hematopoiesis, sex determination, gut development, cell differentiation and proliferation, as well as other essential processes in organisms ranging from yeast to humans [2, 3]. Hence, it is crucial that we understand the relationship of the various bHLH members, and be able to classify them into well-defined categories. These transcription factors, having a signature bHLH structural motif of approximately 60 amino acids and 19 highly conserved amino acids, consist of a basic region followed by two α-helices separated by a loop (HLH) region of variable length [2]. Working as a DNA-binding domain, the two basic domains dimerize to create a DNA interaction surface that recognizes the consensus hexanucleotide sequence, while the HLH domain interacts with other bHLH proteins to form homodimers or heterodimers between different bHLH family members [4, 5].

                In 1997, a phylogenetic analysis based on 122 bHLH sequences resulted in a natural classification of different bHLH transcription factors into four monophyletic protein groups named A, B, C and D in an attempt to functionally classify bHLH proteins [6]. Since more bHLH proteins had been identified in animals, plants and fungi, 44 orthologous families and six higher-order groups had been defined based on phylogenetic analyses to then available bHLH proteins [3, 68]. In addition, after the revision of Simionato et al. in 2007, animal bHLH proteins are classified into 45 families, among which 22, 12, 7, 1, 2 and 1 families are included in high order groups A, B, C, D, E and F, respectively [9]. Briefly, groups A and B bHLH proteins are inclined to bind core DNA sequences typical of E boxes (CANNTG), in which group A recognizes and binds CACCTG or CAGCTG and group B recognizes and binds CACGTG or CATGTTG. Group A bHLH proteins mainly regulate neurogenesis, myogenesis and mesoderm formation, while group B ones mainly regulate cell proliferation and differentiation, sterol metabolism and adipocyte formation, and expression of glucose-responsive genes. Group C proteins, complex molecules with one or two PAS domains following the bHLH motif, tend to bind the core sequence of ACGTG or GCGTG. They are responsible for the regulation of midline and tracheal development, circadian rhythms, and for the activation of gene transcription in response to environmental toxins. Group D proteins correspond to bHLH proteins that are unable to bind DNA due to lack of a basic domain and act as antagonists of group A proteins. Group E proteins, mainly regulating embryonic segmentation, somitogenesis and organogenesis, bind preferentially to sequences referred to as N boxes (CACGCG or CACGAG) and usually contain two characteristic domains named “Orange” and “WRPW” peptide in the carboxyl terminus. Group F proteins have the COE domain which has an additional domain involved in both dimerization and DNA binding. It has only one family, and mainly regulates head development and formation of olfactory sensory neurons [7, 10].

                Due to the pivotal regulatory functions of bHLH proteins displaying in various organisms and the completion of genome sequencing projects for an increased number of organisms, it would be desirable to have a more refined classification scheme of the various types of bHLH motifs, as well as a better understanding of their evolutionary relationships both within and among species. Large numbers of bHLH family members have been the subject of several studies targeting the identification of their full complement encoded by genomes completely sequenced. The putative full set of genes encoding bHLH proteins has been reported to be 8 bHLH genes in Saccharomyces cerevisiae, 16 in Amphimedon queenslandica, 33 in Hydra magnipapillata, 42 in Caenorhabditis elegans, 46 in Ciona intestinalis, 50 in Strongylocentrotus purpuratus, 50 in Tribolium castaneum, 51 in Apis mellifera, 52 in Bombyx mori, 54 in Acyrthosiphon pisum, 57 in Daphnia pulex, 59 in Drosophila melanogaster, 63 in Lottia gigantea, 64 in Capitella sp 1, 68 in Nematodtella vectensis, 70 in Acropora digitifera, 78 in Branchiostoma floridae, 87 in Tetraodon nigroviridis, 104 in Gallus gallus, 107 in Ailuropoda melanoleuca, 114 in Mus musculus, 114 in Rattus norvegicus, 118 in Homo sapiens, 139 in Danio rerio, 162 in Arabidopsis thaliana, and 167 in Oryza sativa[921].

                Ponerine ant, Harpegnathos saltator (Jerdon, 1851), has recently been introduced as a model organism for studying the relationship between stress resistance and longevity of eusocial insects, as well as the role of epigenetics in behavior, aging, and development. Several studies have recently been conducted to elucidate the developmental processes that result in its particular characters [22, 23]. However, the H. saltator bHLH proteins have not yet been studied and characterized in detail. The H. saltator genome is the first ant genome having been sequenced. The draft H. saltator genome assembly sequenced using the Illumina Genome Analyzer platform was submitted by the Beijing Genomics Institute –Shenzhen in August 2010. Moreover, the H. saltator draft genomic assemblies reached scaffold N50 with a size of ~600 kb and covered more than 90% of the genomes [22].

                The comprehensive identification of bHLH protein members encoded in the H. saltator genome would facilitate experimental studies on biological functions of bHLH proteins in the regulation of H. saltator development as well as evolutionary analyses to the diversification of insect bHLH genes. In this study, tblastn searches against H. saltator genome sequence database was conducted using both amino acid sequences of 59 Drosophila melanogaster bHLH (DmbHLH) motifs [17] and the 45 representative bHLH families (Additional file 1) [7] to retrieve candidate bHLH members. Subsequent examination and phylogenetic analysis enabled us to identify the putative full set of bHLH members encoded in H. saltator and to define orthologous families with sufficient confidence. The obtained results are helpful for further investigations into the structure and function of bHLH proteins in the regulation of H. saltator development.

                Results and discussions

                Identification of PabHLH members

                The tblastn searches, intron analysis, manual checking of the 19 conserved amino acid sites, and sequence alignment reveal that there are 57 bHLH members in H. saltator (Additional file 2). The alignment of all 57 PabHLH members is shown in Figure  1, and the phylogenetic tree generated utilizing amino acids of 57 PabHLH motifs and 59 DmbHLH motifs is illustrated in Figure  2. Both figures demonstrate that there are 23, 14, 10, 1, 8 and 1 PabHLH members in group A, B, C, D, E and F, respectively. It can be seen from Figure  1 that sites 23 and 64 of the bHLH motif are the most conserved sites among all PabHLH motifs. Besides, other ten sites, marked with asterisks on top of Figure  1, are also highly conserved. Additionally, Figure  1 indicates that one PabHLH motif PaDys2 has quite special amino acids. Whereas the alignments of all identified bHLH motifs in other insect species have no gaps in the basic and helix 1 regions and only one major gap in the loop region [13, 14], PaDys2 has two additional amino acids (T and P) in helix 1 region. The existence of these amino acids has created an additional gap among aligned PabHLH motifs (Figure  1), indicating certain difference between H. saltator and other insect species. From Figure  2, we found two cases, like PaAse1 and PaAse2 which can form a monophyletic clade with ase from fruit fly, that the two PabHLHs group together with high statistical support to the exclusion of any other sequences and are often orthologs of a single fruit fly motif. This may reveal relatively recent duplications specific to the H. saltator. Besides these characters on Figure  2, two PabHLHs, PaH1 and PaH2, can be related to two D. melanogaster families of orthologs. This may indicate that the diversity of those bHLHs found in both species occurred before the generation of duplications.
                http://static-content.springer.com/image/art%3A10.1186%2F1471-2148-12-165/MediaObjects/12862_2012_2164_Fig1_HTML.jpg
                Figure 1

                Multiple sequence aligment of bHLH motifs of the 57 PabHLH sequences. The scheme at top illustrates the locations and boundaries of the basic, helix 1, loop and helix 2 regions within the bHLH domain following that of Ferre-D’Amare et al. ( 1993). The numbers below the scheme (1 to 75) present the position within the bHLH motif as defined in this study. The shading of the alignment indicates identical residues in black, conserved residues in dark gray and similar residues in light gray. Highly conserved sites are indicated with asterisks on the top. Strigula denote gaps. The family names and high-order groups have been organized according to Table  1 of Ledent et al. ( 2002).

                http://static-content.springer.com/image/art%3A10.1186%2F1471-2148-12-165/MediaObjects/12862_2012_2164_Fig2_HTML.jpg
                Figure 2

                Neighbor-joining phylogenetic tree of 57 PabHLH members with 59 Drosophila melanogaster bHLH members. The NJ tree summarizes the evolutionary relationship between the PabHLHs and DmbHLHs, which has been rooted using OsRa (a rice bHLH motif sequence of R family) as outgroup. This tree is based on a multiple alignment that includes 59 bHLH sequences of D. melanogaster and 57 PabHLH members. For simplicity, branch lengths of the tree are not proportional to distances between sequences. Only bootstrap values more than 50 are shown. The higher-order group labels are in accordance with Ledent et al. ( 2002).

                During our analyses, one sequence “RREIANSNERRRMQSINAGFQSLRSLLPHHEGEKLSKVCIV” (contig number: AEAC01009287.1, coding region from 29454 to 29576) was found to have high similarity with AP4 family. However, the immediately following codon is a stop codon. We consider that it could be a pseudogene or the sequence with a nonsense mutation. But it is also possible that the protein sequence coded by this gene was not accurately predicted.

                Based on bootstrap supports provided by the in-group phylogenetic analyses, the identified PabHLH motifs were subdivided into corresponding bHLH families and named according to nomenclature used by DmbHLH sequences. Although a new nomenclature for bHLH proteins has been proposed recently [24], we adopted nomenclature used in D. melanogaster for facilitating further studies on structural and functional comparison with D. melanogaster. In case that one DmbHLH sequence has two or more H. saltator homologues, we use ‘1’, ‘2’ and ‘3’ etc. to number them. For instance, two homologues of the D. melanogaster Mistr and USF genes were found in H. saltator, respectively. Therefore, these PabHLH genes were named PaMistr1 and PaMistr2, PaUSF1, and PaUSF2, respectively. Names of 57 PabHLHs in accordance with their corresponding D. melanogaster homologues are listed in Table  1.
                Table 1

                A complete list of bHLH genes from Harpegnathos saltator

                No.

                Gene name

                Family

                Fruit fly homolog

                Bootstrap values

                Protein accession No.

                    

                NJ

                MP

                ML

                 

                01

                PaAse1*

                ASCa

                ase

                99

                98

                97

                EFN85365.1

                02

                PaAse2

                ASCa

                ase

                44

                33

                61

                EFN85366.1

                03

                PaDa

                E12/E47

                da

                100

                100

                92

                EFN82122.1

                04

                PaNau

                MyoD

                nau

                100

                99

                57

                EFN79255.1

                05

                PaTap(bp)

                Ngn

                tap (bp)

                99

                97

                84

                EFN75119.1

                06

                PaMistr1

                Mist

                Mistr

                100

                100

                70

                EFN88257.1

                07

                PaMistr2

                Mist

                Mistr

                100

                97

                65

                EFN75769.1

                08

                PaOli

                Beta3

                Oli

                100

                100

                59

                EFN75891.1

                09

                PaCato

                Atonal

                cato

                48

                43

                55

                EFN82083.1

                10

                PaAto

                Atonal

                ato

                98

                94

                75

                Not available

                11

                PaAmos

                Atonal

                amos

                84

                65

                50

                EFN82082.1

                12

                PaNet

                Net

                net

                100

                100

                63

                Not available

                13

                PaMyoR

                MyoRa

                MyoR

                99

                97

                64

                EFN78165.1

                14

                PaSage

                Mesp

                sage

                100

                100

                94

                Not available

                15

                PaPxs

                Paraxis

                Pxs

                93

                77

                88

                Not available

                16

                PaTwi1

                Twist

                twi

                100

                99

                83

                EFN77900.1

                17

                PaTwi2

                Twist

                twi

                63

                43

                73

                EFN77901.1

                18

                PaFer1

                PTFa

                Fer1

                100

                78

                63

                EFN75358.1

                19

                PaFer2

                PTFb

                Fer2

                99

                95

                53

                EFN80609.1

                20

                PaFer3

                PTFb

                Fer3

                100

                100

                88

                EFN77527.1

                21

                PaHand

                Hand

                Hand

                99

                95

                50

                EFN90007.1

                22

                PaSCL

                SCL

                SCL

                100

                100

                59

                EFN82626.1

                23

                PaNSCL

                NSCL

                NSCL

                100

                100

                67

                EFN83537.1

                24

                PaMnt1

                Mnt

                Mnt

                100

                100

                88

                EFN84151.1

                25

                PaMnt2*

                Mnt

                Mnt

                95

                52

                66

                Not available

                26

                PaMax1

                Max

                Max

                100

                98

                86

                EFN76634.1

                27

                PaMax2

                Max

                max

                96

                80

                73

                EFN83237.1

                28

                PaDm

                Myc

                dm

                82

                76

                68

                EFN89178.1

                29

                PaUSF1

                USF

                USF

                100

                89

                95

                EFN78146.1

                30

                PaUSF2

                USF

                USF

                99

                94

                95

                EFN76085.1

                31

                PaMitf

                MITF

                Mitf

                100

                100

                80

                EFN77564.1

                32

                PaCrp1

                AP4

                Crp

                100

                100

                94

                Not available

                33

                PaCrp2*

                AP4

                Crp

                100

                100

                70

                Not available

                34

                PaBmx

                TF4

                bmx

                100

                96

                89

                EFN84400.1

                35

                PaMLX

                MLX

                MLX

                100

                100

                97

                EFN77615.1

                36

                PaSREBP

                SREBP

                SREBP

                100

                100

                70

                EFN85492.1

                37

                PaTai

                SRC

                tai

                100

                99

                82

                EFN80872.1

                38

                PaClk1

                Clock

                clk

                100

                99

                94

                EFN76178.1

                39

                PaClk2*

                Clock

                clk

                100

                100

                90

                Not available

                40

                PaDys1

                AHR

                dys

                100

                100

                82

                Not available

                41

                PaDys2*

                AHR

                dys

                58

                70

                n/m

                Not available

                42

                PaSs

                AHR

                ss

                100

                100

                83

                EFN80844.1

                43

                PaSim

                Sim

                sim

                88

                92

                63

                EFN79346.1

                44

                PaTrh

                Trh

                trh

                100

                94

                98

                EFN81642.1

                45

                PaSima

                HIF

                sima

                95

                94

                94

                EFN75729.1

                46

                PaTgo

                ARNT

                tgo

                100

                100

                99

                Not available

                47

                PaCyc

                Bmal

                cyc

                99

                83

                68

                EFN88377.1

                48

                PaEmc

                Emc

                emc

                99

                83

                74

                EFN83186.1

                49

                PaHey

                Hey

                Hey

                98

                45

                n/m*

                EFN83075.1

                50

                PaStich1

                Hey

                Stich1

                100

                99

                94

                EFN89077.1

                51

                PaH1

                H/E(spl)

                h

                69

                70

                64

                EFN78278.1

                52

                PaH2

                H/E(spl)

                h

                n/m

                47

                n/m*

                EFN78273.1

                53

                PaSide

                H/E(spl)

                side

                99

                100

                94

                EFN79220.1

                54

                PaE(spl)1*

                H/E(spl)

                E(spl) mC(d)

                98

                50

                n/m*

                EFN87932.1

                55

                PaE(spl)2*

                H/E(spl)

                ? - ortholog of AmE(spl)2

                80

                67

                52

                EFN87924.1

                56

                PaE(spl)3*

                H/E(spl)

                ? - ortholog of AmE(spl)3

                100

                96

                99

                EFN87930.1

                57

                Pakn(col)

                COE

                kn (col)

                100

                100

                92

                EFN79194.1

                We named PabHLH genes according to their D. melanogaster homologues. Bootstrap values were obtained from in-group phylogenetic analyses with D. melanogaster or A. mellifera bHLH motif sequences using NJ, MP, and ML algorithms, respectively. OsRa (the rice bHLH motif sequence of R family) was used as the outgroup in each constructed tree. n/m means that a H. saltator bHLH does not form a monophyletic group with any other single bHLH motif sequence. n/m* means that a H. saltator bHLH does not form a monophyletic clade with any specific bHLH motif sequence but forms a monophyletic clade with other bHLH proteins of the same family. * means that orthology of the gene was defined through in-group phylogenetic analyses with bHLH orthologs from A. mellifera.

                Identification of orthologous families

                Orthologous genes in two or more organisms are those that evolved by vertical descent from the same gene in the last common ancestor [25]. Ortholog identification has much uncertainty because of the lack of absolute criterion that can be applied to decide whether two genes are orthologous or not [7]. Nevertheless, in our previous studies [13, 14], in-group phylogenetic analysis was adopted to identify homologues for the unknown sequences that would form a monophyletic clade among themselves. Therefore, a more certain standard based on the criterion used by Ledent et al. was used in this study. That is, we defined bHLH families of orthologs as monophyletic groups which include sequences of a known family and whose monophyly is consistent with the different phylogenetic algorithms and supported by bootstrap values superior to 50 [7, 9, 17].

                We have performed in-group phylogenetic analysis to each of the 57 identified bHLHs, which enabled us to allocate all the identified PabHLHs to defined evolutionary conserved groups of orthology. Figure  3, as an example here, shows distance neighbour-joining (NJ), maximum parsimony (MP), and maximum likelihood (ML) phylogenetic trees constructed with one PabHLH member (PaCrp1) and 10 group B bHLH members from D. melanogaster. PaCrp1 formed monophyletic clade with crp (cropped) sequence of D. melanogaster with bootstrap values of 100, 100 and 94 in NJ, MP and ML phylogenetic trees, respectively. PaCrp1 was therefore considered as an ortholog of fruit fly crp. Similarly, in-group phylogenetic analysis was conducted to each of the identified PabHLH members. All the bootstrap values of constructed NJ, MP and ML trees for each of the identified PabHLH members were listed in Table  1 without displaying the correspondent constructed trees. The majority of these bHLHs could be clearly allocated to the families defined according to bootstrap values of in-group phylogenetic trees. Nevertheless, eight PabHLHs (a significant proportion, about 14%) could not be confidently allocated to the defined families by our phylogenetic analysis with DmbHLHs. They were used to construct trees with Apis mellifera bHLHs (AmbHLH) using the same methods mentioned above. Table  1 showed that orthology of PabHLHs with fruit fly or honey bee bHLHs could be divided into the following categories.
                http://static-content.springer.com/image/art%3A10.1186%2F1471-2148-12-165/MediaObjects/12862_2012_2164_Fig3_HTML.jpg
                Figure 3

                In-group phylogenetic analyses of PaCrp1 . (a), (b), and (c) are NJ, MP, and ML trees, respectively, constructed with one H. saltator bHLH member (PaCrp1) and ten group B bHLH members from D. melanogaster. In all trees, OsRa was used as the outgroup.

                Firstly, among all the 57 PabHLH members, there are 44 bHLH members of which all the bootstrap values ranged from 50 to 100 in constructed NJ, MP and ML trees. Namely, they are PaDa, PaNau, PaTap(bp), PaMistr1, PaMistr2, PaOli, PaAto, PaAmos, PaNet, PaMyoR, PaSage, PaPxs, PaTwi1, PaFer1, PaFer2, PaFer3, PaHand, PaSCL, PaNSCL, PaMnt1, PaMax1, PaMax2, PaDm, PaUSF1, PaUSF2, PaMitf, PaCrp1, PaBmx, PaMLX, PaSREBP, PaTai, PaClk1, PaDys1, PaSs, PaSim, PaTrh, PaSima, PaTgo, PaCyc, PaEmc, PaStich1, PaH1, PaSide and PaKn(col). All these bootstrap values were no lower than the set criterion (50) and thus resulted in assignment of corresponding D. melanogaster homologues for them with sufficient bootstrap support (Table  2).
                Table 2

                Coding regions, intron location and length of 57 PabHLH motifs

                Family

                Gene name

                Genomic coding sequence(s)

                Intron (location,length)

                Group

                  

                Contig no.

                Frame

                Coding region(s)

                  

                ASCa

                PaAse1

                AEAC01008798.1

                +3

                9033-9242

                 

                A

                ASCa

                PaAse2

                AEAC01008800.1

                +2

                11015-11191

                 

                A

                E12/E47

                PaDa

                AEAC01014068.1

                +3

                28419-28447

                Basic: 805 bp

                A

                +1

                29253-29385

                MyoD

                PaNau

                AEAC01019196.1

                −2

                74906-74862

                Helix 1: 1290bp

                A

                −2

                73571-73461

                Ngn

                PaTap(bp)

                AEAC01026729.1

                −1

                32156-31998

                 

                A

                Mist

                PaMistr1

                AEAC01003460.1

                −2

                3518-3456

                Helix 1: 100bp

                A

                −3

                3355-3260

                Mist

                PaMistr2

                AEAC01025732.1

                −1

                1835-1773

                Helix 1: 788bp

                A

                −3

                984-889

                Beta3

                PaOli

                AEAC01025379.1

                +2

                21989-22153

                 

                A

                Atonal

                PaCato

                AEAC01014266.1

                −1

                26350-26192

                 

                A

                Atonal

                PaAto

                AEAC01015400.1

                +2

                188-346

                 

                A

                Atonal

                PaAmos

                AEAC01014265.1

                −1

                11834-11676

                 

                A

                Net

                PaNet

                AEAC01000094.1

                +1

                43-201

                 

                A

                MyoRa

                PaMyoR

                AEAC01020981.1

                −1

                91681-91523

                 

                A

                Mesp

                PaSage

                AEAC01024430.1

                −2

                277-116

                 

                A

                Paraxis

                PaPxs

                AEAC01022136.1

                +3

                27672-27715

                Helix 1: 560bp

                A

                +2

                28276-28390

                Twist

                PaTwi1

                AEAC01021518.1

                −3

                26828-26673

                 

                A

                Twist

                PaTwi2

                AEAC01021518.1

                −3

                48350-48195

                 

                A

                PTFa

                PaFer1

                AEAC01026349.1

                +1

                45976-46134

                 

                A

                PTFb

                PaFer2

                AEAC01016863.1

                −3

                13162-13119

                Helix 1: 410bp

                A

                −2

                12708-12594

                PTFb

                PaFer3

                AEAC01022136.1

                +2

                110825-110905

                Helix 1: 2060bp

                A

                +1

                112966-113043

                Hand

                PaHand

                AEAC01000415.1

                +1

                31600-31758

                 

                A

                SCL

                PaSCL

                AEAC01013335.1

                +2

                41306-41445

                Helix 2: 769bp

                A

                +3

                42215-42233

                NSCL

                PaNSCL

                AEAC01011813.1

                −1

                35707-35685

                Basic: 536bp

                A

                −3

                35148-34998

                Mnt

                PaMnt1

                AEAC01010687.1

                +1

                58000-58008

                Helix 2: 2123bp

                B

                +2

                55730-55876

                Mnt

                PaMnt2

                AEAC01009610.1

                +1

                110044-110202

                 

                B

                Max

                PaMax1

                AEAC01023724.1

                +3

                2178-2336

                 

                B

                Max

                PaMax2

                AEAC01012273.1

                +1

                1648-1803

                 

                B

                Myc

                PaDm

                AEAC01001866.1

                −3

                39047-38889

                 

                B

                USF

                PaUSF1

                AEAC01020973.1

                −2

                90699-90538

                Loop: 88bp

                B

                −3

                90449-90399

                USF

                PaUSF2

                AEAC01025009.1

                −1

                32215-32075

                Loop: 101bp

                B

                −3

                31973-31923

                MITF

                PaMitf

                AEAC01022111.1

                +2

                23396-23417

                Basic: 5715bp

                B

                +2

                29133-29208

                Loop: 7943bp

                +1

                37152-37233

                 

                AP4

                PaCrp1

                AEAC01009287.1

                +3

                29454-29564

                locate on two separate contigs

                B

                AEAC01009292.1

                +2

                42008-42052

                AP4

                PaCrp2

                AEAC01008415.1

                +2

                21659-21817

                 

                B

                TF4

                PaBmx

                AEAC01010529.1

                −1

                64180-64010

                 

                B

                MLX

                PaMLX

                AEAC01022037.1

                −1

                166446-166282

                 

                B

                SREBP

                PaSREBP

                AEAC01008623.1

                −2

                34731-34589

                Helix 2: 82bp

                B

                −3

                34506-34497

                SRC

                PaTai

                AEAC01016429.1

                −3

                7000-6993

                Basic: 2799bp

                B

                −3

                4193-4040

                Clock

                PaClk1

                AEAC01024883.1

                −3

                2390-2386

                Basic: 117bp

                C

                −3

                2268-2121

                Clock

                PaClk2

                AEAC01008322.1

                +3

                17766-17927

                 

                C

                AHR

                PaDys1

                AEAC01000476.1

                −3

                12657-12496

                 

                C

                AHR

                PaDys2

                AEAC01002106.1

                −1

                11804-11649

                 

                C

                AHR

                PaSs

                AEAC01016399.1

                +2

                38537-38698

                 

                C

                Sim

                PaSim

                AEAC01018973.1

                +2

                52010-52171

                 

                C

                Trh

                PaTrh

                AEAC01014876.1

                −3

                10700-10539

                 

                C

                HIF

                PaSima

                AEAC01025720.1

                −1

                31971-31810

                 

                C

                ARNT

                PaTgo

                AEAC01022806.1

                −1

                23646-23485

                 

                C

                Bmal

                PaCyc

                AEAC01003406.1

                +3

                16767-16771

                Basic: 1814bp

                C

                +2

                18586-18742

                Emc

                PaEmc

                AEAC01012314.1

                +1

                2998-3096

                 

                D

                Hey

                PaHey

                AEAC01012628.1

                +1

                61852-62019

                 

                E

                Hey

                PaStich1

                AEAC01002103.1

                +3

                5010-5177

                 

                E

                H/E(spl)

                PaH1

                AEAC01020843.1

                +1

                70384-70389

                Basic: 406bp

                E

                Loop: 272bp

                +2

                70796-70891

                +1

                71164-71235

                H/E(spl)

                PaH2

                AEAC01020833.1

                −2

                8228-8223

                Basic: 301bp

                E

                −3

                7921-7826

                Loop: 3123bp

                −3

                4702-4631

                 

                H/E(spl)

                PaSide

                AEAC01019264.1

                −1

                1124-957

                locate on two separate contigs

                E

                AEAC01019265.1

                −2

                1044-1039

                H/E(spl)

                PaE(spl)1

                AEAC01003976.1

                +1

                4951-4956

                Basic: 1338bp

                E

                +1

                6295-6384

                Loop: 2233bp

                +2

                8618-8695

                 

                H/E(spl)

                PaE(spl)2

                AEAC01003969.1

                −2

                11262-11257

                Basic: 199bp

                E

                −3

                11057-10890

                H/E(spl)

                PaE(spl)3

                AEAC01003972.1

                +2

                36986-37159

                 

                E

                COE

                Pakn(col)

                AEAC01019320.1

                −3

                1427-1427

                Helix 1: 197bp

                F

                   

                −2

                1229-1096

                  

                Secondly, one bHLH member, PaTwi2, had bootstrap value of 43 in MP tree. Nevertheless, it formed monophyletic clade with the same DmbHLH counterpart in NJ and ML tree with bootstrap values of 63 and 73, respectively. Two members, PaAse2 and PaCato, formed monophyletic clade with bootstrap values of 55 and 61 in ML trees, but formed monophyletic clade with weak bootstrap values (33 to 48) in NJ and MP trees. Consequently, we allocated them to defined families of orthologs according to the one or two trees with bootstrap values of over 50.

                Thirdly, one bHLH member, PaHey, formed monophyletic clade in NJ and MP trees with bootstrap values of 98 and 45, respectively, but did not form monophyletic group in ML tree. Another PabHLH member, PaH2, formed monophyletic clade with bootstrap value 47 in MP tree, but did not form monophyletic clade in NJ and ML trees (marked with n/m* or n/m in Table  1). Albeit with insufficient statistical support, we tentatively defined orthologs for them because they all have one or two bootstrap support to testify their orthology to the correspondent D. melanogaster ortholog. Obviously, these classifications can be regarded as arbitrary and ought to be modified upon new data available. From a certain perspective, this phylogenetic divergence of bHLH motif sequences between H. saltator and D. melanogaster probably implies that these two insect species have evolved in quite different circumstances.

                Finally, the remaining 8 members named PaAse1, PaMnt2, PaCrp2, PaClk2, PaDys2, PaE(spl)1, PaE(spl)2 and PaE(spl)3 did not form monophyletic clade or did not have sufficient bootstrap support in forming monophyletic clade with any single D. melanogaster homologue in all three phylogenetic trees constructed. They were identified through constructing phylogenetic trees with AmbHLH family members accordingly. Six members, namely PaAse1, PaMnt2, PaCrp2, PaClk2, PaE(spl)2 and PaE(spl)3, were identified with sufficient confidence for all the bootstrap values were over 50 in all the constructed trees. The rest two members, PaDys2 and PaE(spl)1, formed monophyletic clade in NJ and MP trees with bootstrap values ranging from 50 to 98. We assigned orthologs for them according to the two trees with bootstrap values over 50, though they did not form monophyletic group in ML trees.

                Through prediction by SMART using the full sequence of identified bHLH members whose protein accession number were available (Additional file 3), we found that: a) Among members of group C, there are 4 sequences having one bHLH, one PAC (Motif C-terminal to PAS motifs) [26] and two PAS (PER-ARNT-SIM homology) domains, while EFN88377.1 has one bHLH, and two PAS domains. The remaining one (EFN80844.1) only has bHLH domain. b) For group E, all of the PabHLHs have bHLH and Orange domains, one of which, however, has Orange with scores less significant than the required threshold. And all of them ended with “WRPW” peptide. c) The rest groups were predicted to only have bHLH domains. These results suggest that our analyses are consistent with the previous reports [3, 27, 28], and it is conceivable that these domains may cooperate and thereby confer particular functions on the proteins containing them [9].

                Protein sequences and genomic coding regions of H. saltator bHLH genes

                Protein sequence accession numbers of the 57 identified PabHLH motifs were listed in Table  1. As we have seen, there are only 46 PabHLH motifs whose protein sequence accession numbers were found in H. saltator genome database (shown as ‘EFN’ plus number). Protein sequences of the other 11 PabHLHs, namely PaAto, PaNet, PaSage, PaPxs, PaMnt2, PaCrp1, PaCrp2, PaClk1, PaDys1, PaDys2, and PaTgo, were not found in current database. The coding regions, intron location and length of 57 PabHLH motifs are listed in Table  2. The intron analysis shows that 22 PabHLH members have introns in the coding regions of their bHLH motifs. It should be noted that: a) coding regions of 18 PabHLH motifs have one intron, among which those of 6 PabHLH motifs have introns in the basic region, 7 have introns in the helix 1 region, 2 have introns in the loop region, and 3 have introns in the helix 2 region. b) Coding regions of 4 PabHLH motifs have two introns, all of which are in the basic and loop regions. Thus, altogether, coding regions of these 22 PabHLH motifs have 26 introns. In addition, 2 PabHLHs named PaCrp1 and PaSide locate on two separate contigs in the genome (Table  2). The longest intron in coding regions of PabHLH motifs is 7,943 bp (base pairs), the shortest one is only 82 bp, and the average length of introns is 1,391 bp. While in pea aphid, fruit fly and honey bee, there are 26, 18 and 9 bHLH members having introns in coding regions of their bHLH motifs, and the total number of introns identified is 34, 20 and 9 with the longest one of 30,718, 11,845 and 4,460 bp, the shortest one of 62, 57 and 72, and the average length of 4,193, 1,082 and 1,326 bp, respectively [14, 16].

                In summary, the number of PabHLHs having introns is more than many other insect species, and they are found to have introns with average length only inferior to those of pea aphid. Moreover, PabHLHs have the shortest length of intron only higher than those of fruit fly and honey bee. PabHLH genes are more intron-dense than those of many other insects, indicating that H. saltator either gained introns at a faster rate or lost introns at a slower rate than other insects [29]. Previously hypothesized mechanisms of intron gain mainly involve intron transposition [30], transposon insertion [31], tandem genomic duplications [32], intron transfer [33], insertion of a Group II intron [30], intron gain during double strand break repair [34] and intronization [35, 36]. Three previously hypothesized mechanisms of intron loss include Reverse Transcriptase-Mediated Intron Loss (RTMIL) [37], Meiotic recombination [29] and genomic deletions [38]. Notably, the genome of H. saltator contains copies of specific transposable element (TE) families, which differs significantly with other species (i.e. Camponotus floridanus and A. mellifera have very few TEs) [22, 39]. We infer that there may be some relationships between the formation of intron in PabHLHs and TEs. Nevertheless, whether the more intron-dense introns are due to growing faster or losing slower needs further investigations.

                The existence of EST (expressed sequence tag) sequence corresponding to identified bHLH motifs is an indication of genuine bHLH gene at least at the transcriptional level. However, we were unable to find any EST sequences for our identified PabHLHs due to the unavailability of H. saltator EST database at time of our survey. Therefore, further verification of our identified PabHLH members awaits expansion of H. saltator nucleotide sequence data and experimental cloning of the genuine PabHLH genes. It would thus be of particular interest to study whether the bHLH family members identified in H. saltator are expressed during various developmental processes and how their expression patterns may be related to those of other insect counterparts.

                bHLH repertoire of the H. saltator and other insect species

                The above searches and analyses enabled us to define orthologs of families for 57 PabHLHs. This figure is comparable with 50, 51, 52, 54 and 59 bHLH members in the red flour beetle, honey bee, domestic silkworm, pea aphid and fruit fly, respectively (Table  3). According to Table  3, all of these five insect species lack genes of families Oligo, MyoRb, and Figα, and many of the families have the same number of genes, such as E12/E47, Ngn, Beta3, Net, Paraxis, Hand, PTFa, SCL, NSCL, SRC, Myc, SREBP, ARNT, Trh, HIF, Emc and COE. The fact that comparable number of bHLH families and similar orthologs were detected strongly suggests that, despite our analysis was made on a draft version of the H. saltator genome sequence, the set of PabHLH we retrieved is likely to be almost complete, and hence gives a highly accurate view of the bHLH repertoire of a ponerine ant. The major obvious difference, other than total genes, is the discrepancy of H/E (spl) family members. D. melanogaster have 11 to 12 H/E(spl) genes while other insects have 5 to 6. H. saltator has fewer genes in families ASCa, and Clock than D. melanogaster. It is conspicuous that H. saltator has one more gene in families Twist, Mnt, Max, USF, AHR and AP4 than most other insect species previously reported. Thirteen PabHLH families have more than one member (accounted for about 29% of the families), while in most other insects, families with more than one member are fewer (mean value 16%; range 13% to 20%). This suggests that some of the H. saltator bHLH genes have been originated through duplications. Moreover, a feature to be noted is that neither of the two families, namely Delilah and MyoRb, was found. Whether H. saltator does have fewer members of these families, or if it was due to incompleteness of the genome sequences remains for further exploitation. Therefore, it can be thought that additional bHLH members may be found after a newer and higher quality version of H. saltator genome sequences is released.
                Table 3

                A comparison on bHLH family members from six insect species

                Group

                Family name

                P.a.

                A.m.

                B.m.

                T.c.

                D.m.

                A.p.

                A

                ASCa

                2

                2

                4

                3

                4

                0

                A

                ASCb

                0

                0

                0

                0

                0

                1

                A

                MyoD

                1

                1

                1

                1

                1

                0

                A

                E12/E47

                1

                1

                1

                1

                1

                1

                A

                Ngn

                1

                1

                1

                1

                1

                1

                A

                NeuroD

                0

                0

                0

                1

                0

                0

                A

                Atonal

                3

                3

                1

                3

                3

                3

                A

                Mist

                2

                2

                1

                1

                1

                2

                A

                Beta3

                1

                1

                1

                1

                1

                1

                A

                Oligo

                0

                0

                0

                0

                0

                0

                A

                Net

                1

                1

                1

                1

                1

                1

                A

                Delilah

                0

                0

                1

                2

                1

                1

                A

                Mesp

                1

                1

                1

                0

                1

                1

                A

                Twist

                2

                1

                1

                1

                1

                1

                A

                Paraxis

                1

                1

                1

                1

                1

                1

                A

                MyoRa

                1

                1

                1

                1

                1

                1

                A

                MyoRb

                0

                0

                0

                0

                0

                0

                A

                Hand

                1

                1

                1

                1

                1

                1

                A

                PTFa

                1

                1

                1

                1

                1

                1

                A

                PTFb

                2

                1

                1

                2

                2

                2

                A

                SCL

                1

                1

                1

                1

                1

                1

                A

                NSCL

                1

                1

                1

                1

                1

                1

                B

                SRC

                1

                1

                1

                1

                1

                1

                B

                Figα

                0

                0

                0

                0

                0

                0

                B

                Myc

                1

                1

                1

                1

                1

                1

                B

                Mad

                0

                0

                0

                1

                0

                1

                B

                Mnt

                2

                1

                1

                1

                1

                1

                B

                Max

                2

                1

                1

                1

                1

                3

                B

                USF

                2

                2

                1

                1

                1

                1

                B

                MITF

                1

                1

                1

                1

                1

                0

                B

                SREBP

                1

                1

                1

                1

                1

                1

                B

                AP4

                2

                1

                1

                1

                1

                1

                B

                MLX

                1

                1

                1

                0

                1

                1

                B

                TF4

                1

                1

                1

                1

                1

                2

                C

                Clock

                2

                2

                3

                2

                3

                2

                C

                ARNT

                1

                1

                1

                1

                1

                1

                C

                Bmal

                1

                1

                2

                1

                1

                1

                C

                AHR

                3

                2

                3

                1

                2

                2

                C

                Sim

                1

                1

                1

                0

                1

                1

                C

                Trh

                1

                1

                1

                1

                1

                1

                C

                HIF

                1

                1

                1

                1

                1

                1

                D

                Emc

                1

                1

                1

                1

                1

                1

                E

                Hey

                2

                2

                2

                1(2?)

                1(2?)

                3

                E

                H/E(spl)

                6

                6

                5

                5(6?)

                11(12?)

                6

                F

                COE

                1

                1

                1

                1

                1

                1

                 

                Total number of bHLH members

                57

                51

                52

                50

                59

                54

                 

                Number of bHlH families with two or more members

                13

                8

                6

                6

                6

                9

                Data of P.a. (ponerine ant) were from this study. Those of A.m. (Apis mellifera) and B.m. (Bombyx mori) were from Wang et al. 2007, 2008. Those of T.c. (Tribolium castaneum) and D.m. (Drosophila melanogaster) were from Simionato et al. 2007. Those of A.p. (Acyrthosiphon pisum) were from Dang et al. 2011.

                We also executed several additional alignments consisting of only those bHLH sequences that belong to a particular family from 6 insect species above mentioned (Additional file 4). Based on these alignments, the in-family NJ trees were constructed (see Materials and methods) which has been rooted using a fruit fly bHLH sequence from the related family as outgroup. From our phylogenetic analyses (the trees not shown), 34 PabHLHs and AmbHLHs formed monophyletic clade with high bootstrap values (55 to 100), while the members of other insect species were fewer. So we concluded that the PabHLH genes, to a certain extent, have closer phylogenetic relationships with A. mellifera than with other insect species. Additionally, figure  4 shows a typical phylogenetic tree of a family containing the E(spl) family of the five insect species. The members of fruit fly Esplm3, EsplmBg, EsplmAb and Esplm7 clustering together may reveal that these are the result of species-special duplication.
                http://static-content.springer.com/image/art%3A10.1186%2F1471-2148-12-165/MediaObjects/12862_2012_2164_Fig4_HTML.jpg
                Figure 4

                Evolutionary relationships among E(spl) family members from six insect species. This tree is based on a multiple alignment that includes all members of E(spl), which has been rooted using the closely related Hey gene from D. melanogaster as outgroup. And only bootstrap values more than 50 are shown.

                Conclusions

                By utilizing the 45 representative bHLH domains and 59 identified DmbHLHs as query sequences, 57 bHLHs encoded in H. saltator genome sequences were identified. It was necessary to use DmbHLH sequences as query motifs to detect six additional bHLHs found in H. saltator, namely PaCato, PaAmos, PaCrp2, PaDys1, PaStich1 and PaH2, respectively. Since the 45 representative bHLH sequences were mainly from mouse [9, 17], it was more reasonable that we assign relationships according to phylogenetic analysis with DmbHLH members. Additionally, for having no corresponding orthologous genes in D. melanogaster, orthology of 8 bHLHs, namely PaAse1, PaMnt2, PaClk2 PaDys2, PaE(spl)1, PaE(spl)2 and PaE(spl)3, were defined by in-group phylogenetic analyses with A. mellifera bHLHs. The in-family phylogenetic analyses suggest that the PabHLH genes have closer phylogenetic relationships with A. mellifera than others. Among all PabHLH members, protein sequences of 11 PabHLH motifs were not found in any protein databases. We must however caution that we might have missed some bHLHs and/or that we might have included bHLH domains from some pseudogenes. Nevertheless, these data will provide information for further research to obtain a qualitatively accurate assessment of bHLH complement from the information available.

                Methods

                H. saltator bHLH sequence search and primary selection

                Candidate genomic sequences encoding bHLH motifs were identified using BLAST, NetGene2 and EditSeq program (version 5.01), prepared and improved with manual checking and phylogenetic analysis. As a starting point, both lists of 59 DmbHLH motifs and the 45 representative bHLH families were retrieved from the additional files of previous reports [17]. Each sequence was used as a query sequence to perform tblastn search against H. saltator genome sequence database ( http://​www.​ncbi.​nlm.​nih.​gov/​sutils/​genom_​table.​cgi?​organism=​insects). The expect value (E) was set at 10 in order to detect all possible bHLH sequences. Redundant sequences were manually identified and subsequently discarded on purpose of keeping only one sequence with the same contig number, reading frame, and coding regions. Next, the sequences were examined again to check whether the obtained amino acids have covered the full bHLH motif or not. If not, the corresponding subject nucleotide sequence was retrieved and translated using EditSeq program (version 5.01) of the DNAStar package to add the missing amino acids on two ends of this motif. In case where a query sequence composed of two or three H. saltator coding regions, intron splice sites were assessed using the online program NetGene2 ( http://​www.​cbs.​dtu.​dk/​services/​NetGene2/​) to find location of intron between the separate coding regions.

                Moreover, in order to detect whether the retrieved bHLH sequence has corresponding protein sequences deposited in GenBank, each of the retrieved candidate bHLH sequences was used to make similarity searches using blastp algorithm against the NCBI nr database by limiting the query organism to H. saltator. And tblastn search was conducted against the NCBI Expressed Sequence Tag (EST) database to examine whether there were ESTs corresponding to the identified H. saltator bHLHs.

                Finally, each obtained sequence was examined for their amino acid residues at the 19 conserved sites [40] by manual checking. Accordingly, a sequence with less than 9 mismatches could be a potential bHLH motif [41]. Therefore, sequences having no less than 10 conserved amino acid residues among the 19 conserved sites were regarded as potential PabHLH (ponerine ant bHLH) members, except for Emc and COE family members which have around 30 and 50 amino acids in their HLH motif respectively and thus the minimum conserved amino acids were adjusted to 5 and 8 respectively. Sequences failing to meet the above requirements were discarded.

                Multiple sequence alignments

                To examine sequence features of these PabHLH domains, we performed multiple sequence alignment of all the potential bHLH sequences improved by the aforementioned approaches using Clustal W program (version 5.0) implemented in MEGA 5 [42] using the default settings. The aligned PabHLH motifs were highlighted in GeneDoc Multiple Sequence Alignment Editor and Shading Utility (Version 2.6.02) [43] and then copied to rich text file (RTF) for further annotation.

                Phylogenetic analysis

                Three different algorithms were employed for phylogenetic reconstruction: distance neighbour-joining (NJ), maximum parsimony (MP), and maximum likelihood (ML). In general, the phylogenetic trees constructed by the different algorithms were congruent and displayed very similar topologies. First, distance trees were constructed with the neighbor-joining (NJ) algorithm [44] using PAUP 4.0 Beta 10 [45] relying on the step matrix constructed from Dayhoff PAM 250 distance matrix by R. K. Kuzoff ( http://​paup.​csit.​fsu.​edu/​nfiles.​html). Each PabHLH motif sequence was then used to conduct in-group phylogenetic analysis with DmbHLH motif sequences. The in-group phylogenetic trees were performed with NJ and MP algorithms implemented in PAUP program, as well as with ML algorithm using the program TreePuzzle 5.2 [46]. The NJ tree was bootstrapped with 1,000 replicates to provide information about their statistical reliability, while the MP analysis was generated with heuristic search of 100 bootstrap replicates. For ML reconstruction, the parameters were set as follows: quartet-puzzling tree-search procedure, 25,000 puzzling steps and the substitution model set to Jones-Taylor-Thornton [47]. Other parameters were of default values. Additionally, all members from each bHLH family of ponerine ant, red flour beetle, honey bee, domestic silkworm, pea aphid and fruit fly were used to perform phylogenetic analyses, which were termed as in-family phylogenetic analysis because the bHLH motifs for a particular analysis were from the same bHLH family. Each in-family phylogenetic tree was rooted using fruit fly bHLH sequence from a different but related family.

                Domain predicting

                In order to further ascertain the reliability of the retrieved motifs and to examine whether the full-length protein sequences, especially those of Group C, E and F, contain additional characteristic domains, we carried out the predictions of protein domain architectures using Simple modular architecture research tool (SMART, http://​smart.​embl.​de/​) available online [48, 49].

                Abbreviations

                Pa: 

                Ponerine ant, Harpegnathos saltator

                bHLH: 

                Basic helix-loop-helix

                PabHLH: 

                Ponerine ant bHLH

                Am: 

                Apis mellifera

                Ap: 

                Acyrthosiphon pisum

                Bm: 

                Bombyx mori

                Dm: 

                Drosophila melanogaster

                Tc: 

                Tribolium castaneum

                Declarations

                Acknowledgments

                We are grateful to professor Bin Chen of Jiangsu University and two anonymous reviewers for their constructive comments on our manuscript. This work was supported by Scientific Research Promotion Fund for the Talents of Jiangsu University (No. 09JDG029) and China National “973” Key Scientific Program (No. 2012CB114604).

                Authors’ Affiliations

                (1)
                Institute of Life Sciences, Jiangsu University
                (2)
                School of Food and Biological Engineering, Jiangsu University

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