Open Access

Identification and in silico analysis of cattle DExH/D box RNA helicases

  • Manish Kumar Suthar1,
  • Mukul Purva1,
  • Sunil Maherchandani1 and
  • Sudhir Kumar Kashyap1Email author
SpringerPlus20165:25

https://doi.org/10.1186/s40064-015-1640-0

Received: 9 July 2015

Accepted: 20 December 2015

Published: 7 January 2016

Abstract

The helicases are motor proteins participating in a range of nucleic acid metabolisms. RNA helicase families are characterized by the presence of conserved motifs. This article reports a comprehensive in silico analysis of Bos taurus DExH/D helicase members. Bovine helicases were identified using the helicase domain sequences including 38 DDX (DEAD box) and 16 DHX (DEAH box) members. Signature motifs were used for the validation of these proteins. Putative sub cellular localization and phylogenetic relationship for these RNA helicases were established. Comparative analysis of these proteins with human DDX and DHX members was carried out. These bovine helicase have been assigned putative physiological functions. Present study of cattle DExH/D helicase will provides an invaluable source for the detailed biochemical and physiological research on these members.

Keywords

RNA helicasesDEAD boxBioinformaticsBovine Bos taurus

Background

A fundamental cellular action of RNA helicases is to unwind nucleic acid duplexes and thus, they are required for different cellular processes involving RNA. Among these helicases several members perform their functions in pre-mRNA processing and ribosome biogenesis (Linder 2006). The DEAD and DEAH are the subgroups of the DExH/D family (Staley and Guthrie 1998). The DDX code is used for DEAD box and DHX is used for DEAH box. The basis of nomenclature of these DExH/D helicases is the composition of conserved amino acids in their motif II. DEAD-box and DEAH-box, helicases have D-E-A-D (Asp, Glu, Ala and Asp) and D-E-A-H (Asp, Glu, Ala and His) amino acids respectively at this motif. These proteins have role in RNA metabolism viz. transcription, translation, RNA editing and folding, nuclear transport, RNA degradation and RNA-ribosomal complex formations (Linder and Daugeron 2000; Patel and Donmez 2006). These helicases belong to superfamily 2 (SF2) of the six super families in which all the helicases have been classified (Caruthers and McKay 2002; Tanner and Linder 2001). DExD/H-box proteins have been reported from all the living organisms (Umate et al. 2011; Tuteja and Tuteja 2004a, 2004b; Hartung et al. 2000). The core of these enzymes contains two RecA-like domains separated by a short linker. The N-terminal and C-terminal domains are designated as DEAD-domain and helicase domain respectively (Cordin et al. 2006; Pyle 2008). These domains participate in RNA (substrate) binding and ATP hydrolysis. Alignments of the protein sequences obtained from various organisms have revealed nine highly conserved motifs in DEAD-box proteins (Q, I, Ia, Ib, and II–VI) and eight in DEAH-box proteins I, Ia, Ib, II, III, IV, V and VI (Tuteja and Tuteja 2004a, 2004b; Tanner et al. 2003). Among these motifs, motif II (or Walker B motif) along with motif I (or Walker A motif) and Q-motif are necessary for ATP binding and hydrolysis (Tanner et al. 2003) whereas, motifs Ia, Ib, II, IV and V may be involved in RNA binding (Svitkin et al. 2001).

Genome sequencing of variety of organisms have revealed the presence of different numbers of DExH/D helicases. In a genome-wide comparative study 161, 149, 136 and 213 different RNA helicase genes have been identified in Arabidopsis thaliana, Oryza sativa, Zea mays and Glycine max respectively (Xu et al. 2013). Also, 31 DEAD and 14 DEAH putative RNA helicases have been reported from human beings (Umate et al. 2011).

Recently, Steimer and Klostermeier summarised involvement of RNA helicases in infection and diseases (Steimer and Klostermeier 2012). For example dysregulation of these helicases has been linked to a wide variety of cancers. In addition, these proteins have a role in the replication of viruses such as Foot and mouth disease virus infection in cattle and HIV virus in human beings. RNA helicases A (DHX9) has been associated with cattle FMD disease (Radi et al. 2012; Lawrence and Rieder 2009). We can reveal prognostic and diagnostic markers and identify potential drug targets by characterizing these helicases.

Cattle are economically important domesticated ungulates. Phylogenetic analysis has shown a distant clad for cattle as compared to humans and rodents (Murphy et al. 2004) and around 800 breeds have been established serving as resource for the genetics of complex traits studies. The genome sequence for domesticated cattle (Bos taurus) was assembled and published in 2009 (The Bovine Genome Sequencing and Analysis Consortium 2009). The sequence reveals presence of a minimum 22,000 genes in cattle. In the present study, sequenced cattle genome was used to evaluate the number of DEAD-box and related family proteins which might be present, along with their phylogeny. The composition of these bovine motor proteins have also been analysed. In silico analysis of bovine DExH/D helicases provided the putative role of these proteins in various RNA metabolism processes which might be operating in Bos taurus.

Methods

Database search and enlistment of RNA helicases

The sequences for DExH/D family members encoded by Bos taurus were downloaded from NCBI/BLAST (http://www.ncbi.nlm.nih.gov.nih.gov). Amino acid sequence of eIF4A1 (Swiss-Prot Id-Q3SZ54) was obtained first from Swiss-Prot using the key words eIF4A1 Bos taurus. The input sequence so obtained was used in the Cow RefSeq protein database available at NCBI/BLAST home. The cow genome sequences were searched using program BLASTP-Compare protein sequence against ‘BLAST Cow sequences’ resource. Finally tentative lists of DExH/D family members were compiled and all proteins (DExH/D family members) were assigned unique Swiss-Prot IDs, protein names and gene names. After identification of bovine RNA helicases their phylogenetic analysis was carried out along with helicases of other animals of veterinary importance like horse, pig and sheep. For this key words DEAD and DEAH helicase along with animal name were used to download homologs from pig, horse and sheep from Swiss-Prot database for phylogenetic analysis of these DExH/D helicases vis a vis bovine helicases. The amino acid sequences of both families of RNA helicases were aligned and the neighbour-joining method in MEGA 5.0 was applied to examine their evolutionary relationship (Tamura et al. 2011).

Specific sequences of Bos taurus were used for BLASTP search against human homologs as described above to compare their homology. Protein sequences were validated by the presence of signature motifs. Predictive molecular weight and isoelectric point for the RNA helicases were calculated from Sequence Manipulating Suite (http://www.bioinformatics.org/sms2/). Protein localization was studied using WoLF PSORT (http://www.genscript.com/psort/wolf_psort.html) program.

Motif identification and phylogenetic analysis

The signature motifs for the protein family were identified. Protein sequences of DEAD and DEAH members were first aligned using ClustalW2 program available at http://www.ebi.ac.uk/Tools/msa/clustalw2/ and alignment files were downloaded. Conserved motifs in bovine DExH/D were also identified using the MEME suite (version 4.9.1) at meme.nbcr.net/meme/cgi-bin/meme.cgi. Finally list of signature motifs was generated. Phylogenetic analysis was performed using MEGA5 program (http://www.megasoftware.net/) by the Neighbour-Joining method (NJ) with parameters; complete deletion option, p-distance and bootstrapping method with 1000 replicates (Tamura et al. 2011). Final image was obtained using the MEGA5 program. Domain analysis was performed using the program Scan Prosite (http://expasy.org) and these domain structures were used in the figures.

Results and discussion

Identification and validation of Bos taurus DExH/D family members

Genomes of all organisms have genes encoding RNA helicases. Although various comprehensive analyses of these helicases are available in various organisms, limited studies have been conducted on the role of RNA helicases in cattle. The studies of biological function of cattle RNA helicases can unravel their roles and can help in understanding different diseases in cattle and also help in improving economically important traits. Fifty four DExH/D family members of RNA helicases were identified in Bos taurus in the present study, amongst which 38 members belonged to DDX family (DEAD) (Table 1) and 16 members to DHX family (DEAH) of RNA helicases (Table 2). Further analysis of cattle helicase sequences with MEME suite suggested the pattern of amino acids occurrence in signature motifs validating the protein family members. Besides characteristic residues of motifs, some residues were found to be conserved around each motif of various DExH/D family members. The 38 bovine DDX members identified were DDX1, DDX3X, DDX3Y, DDX4, DDX5, DDX6, DDX10, DDX17, DDX18, DDX19A, DDX19B, DDX20, DDX21, DDX23, DDX24, DDX25, DDX27, DDX28, DDX31, DDX39A, DDX39B, DDX41, DDX42, DDX43, DDX46, DDX47, DDX49, DDX50, DDX51, DDX52, DDX53, DDX54, DDX55, DDX56, DDX59, eIF4AI, eIF4AII and eIF4AIII (Table 1). In all, 9 motifs (Q, I, Ia, Ib, II, III, IV, V and VI) were identified in these proteins which are shown in Fig. 1. The signature motifs in DDX protein showed consensus sequences as GFxxPxxIQ (Q), AxxGxGKT (I), PTRELA (Ia), TPGR (Ib), DExD (II), SAT (III), FVxT (IV), RGxD (V) and HRxGRxxR (VI). In the case of DDX49 three motifs namely; TPGR, DExD and SAT were found missing (Fig. 1). The 16 DHX members that could be identified were DHX8, DHX9, DHX15, DHX16, DHX29, DHX30, DHX32, DHX33, DHX34, DHX35, DHX36, DHX37, DHX38, DHX40, DHX57 and DHX58 (Fig. 2). Consensus sequences GxxGxGKT (I), TQPRRV (Ia), TDGML (Ib), DExH (II), SAT (III), FLTG (IV), TNIAET (V) and QRxGRAGR (VI) were found in the members of DHX proteins. Some motifs in two DHX members i.e. DHX32 and DHX58 were not found (Fig. 2). In protein DHX32, SAT, TNIAET and QRxGRAGR motifs were absent, and instead of motif DExH; DDIH motif was observed. In DHX58 conserved motif DECH was observed and remaining motifs were missing. QRxGRAGR motif was not observed in the DHX38 protein (Fig. 2). Four members i.e. DHX32, DHX58, DHX38, and DDX49 showed variable conserved motifs and need biochemical evidence for confirmation. Figure 3 describes patterns in different motifs of DDX and DHX helicases using Hidden Markov Model (HMM). In Fig 3a, b position specific probability is represented by the size of particular amino acid residue in different motifs, larger the size more will be probability of occurrence.
Table 1

Summary of the features of the Bovine DDX member proteins

Bos Taurus

Human

Isoelectric point

Molecular weight (kDa)

Localization

% Coverage with human

% Identity with human

DDX1

DDX1

7.23

82.43

C,N

100

97

DDX3X

DDX3X

7.2

73.15

N

100

99

DDX3Y

DDX3Y Isoform2

7.39

73.17

N

100

91

DDX4

DDX4 Isoform1

5.96

79.46

N,C

100

91

DDX5

Dead box polypeptide 5

9.21

69.16

N

100

100

DDX6

DDX6

8.93

54.39

N

99

99

DDX10

DDX10

9.17

101.18

N

100

89

DDX17

DDX17 Isoform1

8.75

72.33

N,C

100

99

DDX18X1

DDX18

10.04

75.13

N,M

100

90

DDX19A

DDX19A

6.72

54.00

C,N,

100

97

DDX19B

DDX19B Isoform1

8.54

54.46

M,N,C

95

98

DDX20

Dead box polypeptide 20

6.77

92.71

N,C

100

88

DDX23

DDX23

10.22

95.67

N

100

99

DDX24

DDX24

10.01

94.53

N

100

81

DDX25

DDX25

6.33

54.63

C,N

100

93

DDX27

DDX27

9.89

87.10

N

100

95

DDX28

DDX28

10.75

60.02

M,C,N

99

85

DDX31

DDX31

10.43

80.87

N

99

79

DDX39A

DDX39A

5.39

49.15

C,N

100

96

DDX39B

DDX39B

5.38

48.97

C,N

100

99

DDX41

DDX41

6.94

69.83

C,N,M

100

99

DDX42

DDX42

7.28

107.56

N,C

96

95

DDX43

Dead box polypeptide 43

8.77

72.04

N

99

76

DDX46

DDX46 IsoformX1

9.87

117.46

N,C

100

99

DDX47

DDX47 IsoformX1

9.64

50.92

N

100

96

DDX49

DDX49

9.82

44.39

C,N,M

99

91

DDX50

Dead box polypeptide 50

9.64

82.60

N,C

100

97

DDX51

DDX51

7.56

60.69

N,C

98

82

DDX52

DDX52

10.32

67.52

N,C

100

91

DDX53

DDX53

9.88

68.47

N

99

68

DDX54

DDX54

10.68

102.72

N

94

90

DDX55

DDX55

9.83

68.61

N,C

100

94

DDX56

DDX56 Isoform1

9.02

61.27

N,C,M

100

93

DDX59

DDX59

8.03

67.45

N,C

100

77

EIF4AI

EIF4AI Isoform1

5.12

46.15

N

100

100

EIF4AII

EIF4AII

5.13

46.41

N

100

100

EIF4A-III

EIF4A-III

6.69

46.85

N,M

100

99

Nucleolar RNA Hel2

Isoform1(DDX21)

9.87

87.25

N,C

100

89

N, M and C represent Nuclear, Mitochondrial and Cytoplasmic localization, respectively

Table 2

Summary of the features of the Bovine DHX member proteins

Bos Taurus

Human

Isoelectric Point

Molecular weight (kDa)

Localization

% Coverage with human

% Identity with human

DHX8

DHX8

8.33

140.28

N

99

98

DHX9

Helicase A

6.88

141.97

N

90

95

DHX15

DHX15

7.48

90.95

N

100

99

DHX16

DHX16 Iso1

6.39

119.88

N,C

100

98

DHX29

DHX29

8.67

155.28

N

99

93

DHX30

DHX30 Iso1

8.61

135.97

M,C,N

100

97

DHX32

DHX32

4.79

83.88

C,N

100

89

DHX33

DHX32 Iso1

9.23

79.75

N,C

98

92

DHX34

DHX34

7.96

128.80

N,C

100

88

DHX35

DHX35 Iso1

8.66

78.89

N

99

96

DHX36

DHX36 Iso1

7.87

114.85

N,M

100

92

DHX37

DHX37

8.93

129.02

N,C,M

100

85

DHX38

PRP16

6.55

140.19

N

100

95

DHX40

DHX40 Iso1

8.83

88.52

N,C

100

99

DHX57

DHX57

7.69

155.76

N,C

96

91

DHX58

DHX58

8.63

77.19

C,N

100

83

N, M and C represent Nuclear, Mitochondrial and Cytoplasmic localization, respectively

Fig. 1

The amino acid sequence of conserved motifs constituting the RNA helicases of bovine DDX proteins

Fig. 2

The amino acid sequence of conserved motifs constituting the RNA helicases of bovine DHX proteins

Fig. 3

The schematic diagram of motifs of DExH/D helicases. a and b represent motifs for bovine DEAD and DEAH proteins respectively. The schematic diagrams were derived from MEME suite and generated automatically by Meme software based on scores

Phylogenetic analysis

Phylogenetic analysis of DExH/D helicases was performed to elucidate evolutionary relationship. On analysing bovine helicase with that of horse, pig and sheep (Fig. 4a, b) it was observed that some DEAD box helicase family members could be subdivided into nine subgroups in all the species taken into consideration. However, DDX 6, DDX 10, DDX 11, DDX 24, DDX 26, DDX 27, DDX28, DDX 31, DDX 41, DDX 47, DDX49, DDX 51, DDX52, DDX 54, DDX 55, DDX 56, DDX58 and DDX 59 members of DEAD box of all these species could not be included in above nine subgroups (Fig. 4a). Similarly, DHX family members could also be subdivided into four subgroups for all the species (Fig. 4b). However, DHX15, DHX32 and DHX40 could not be included in the any of these four subgroups (Fig. 4b). The extent of similarity indicates toward conserved structure of DExH/D helicases in all the species studied during evolution but their functions remained to be defined by biochemical analysis. In second analysis, relationship amongst bovine helicases was carried out (Fig. 5a, b for DDX and DHX respectively). Phylogenetic analysis established close relationship between different members. The closely related members within DDX subfamily are DDX17-DDX5, DDX43-DDX53, DDX42-DDX46, DDX4-DDX3X-DDX3Y, DDX41-DDX59, DDX39A-DDX39B, DDX19A-DDX19B, EIF4A members, DDX10-DDX18, DDX56-DDX51, DDX47-DDX49, DDX27-DDX54 and DDX50-DDX21. Similarly, within DHX members DHX8-DHX16, DHX33-DHX35, DHX15-DHX32 and DHX36-DHX57 show close relationship. All these members occur as separate clades.
Fig. 4

Phylogenetic analysis of RNA helicases from cattle, pig, horse and sheep. a and b represent DEAD box and DEAH box helicases from four species respectively. DEAD and DEAH amino acid sequences were aligned with ClustalW, and phylogenetic tree was constructed using the neighbour joining method in MEGA 5.0 software

Fig. 5

Phylogenetic analysis of Bovine DExH/D helicases. a and b represent analysis of bovine DEAD and DEAH respectively

In Silico Characterization of Bovine DExH/D family members

Putative molecular weights and isoelectric points of bovine DExH helicases were determined in silico (Tables 1 and 2). Similarly predictive subcellular localizations of these proteins were examined (Tables 1 and 2). These helicases varied in their isoelectric point and molecular subunit mass. Isoelectric point of DDX members varied from 5.12 (EIF4AI) to 10.68 (DDX54) whereas pI for DHX members ranged between 4.79 (DHX32) and 9.23 (DHX33). 24 DDX and 8 DHX members had pI above 8. Molecular mass for these helicases ranged between 44.39 kDa (DDX49) and 117.46 kDa (DDX46) in case of DDX members and between 77.19 kDa (DHX58) and 155.76 kDa (DHX57) for DHX members. The predictive pI value and molecular mass will help in isolation and purification leading to further characterization of these helicases. Analysis with WoLF PSORT program indicated that cattle RNA helicases are localized in the nucleus, cytoplasm and mitochondria (Tables 1 and 2).

Comparative analysis of human and bovine DExH/D family members and putative function assignment

Bos taurus has a 2.86 billion bp long genome with a minimum of 22,000 genes (The Bovine Genome Sequencing and Analysis Consortium 2009). Similarly, 2.91 billion bp long human genome has around 20,000–25,000 genes (International Human Genome Sequencing C 2004). Cattle genome encodes all orthologs of human DExH/D family members. Bovine DEAD box RNA helicases has typically Q motif, ATP binding and Helicase C-terminal domains as found in human helicases. Domain structures of bovine DExH/D RNA helicases as compared with that of human helicases indicated high similarity between the two species (Figs. 6 and 7). Despite this identity DDX17, DDX18, DDX24, DDX27, DDX31, DDX42, DDX49, DDX51, DDX53 and DDX54 show difference in positions of domains as compared to human helicases (Fig. 6). In bovine DDX49 typically overlapping of ATP binding and Helicase domain was observed. Interestingly, both bovine and human DHX32 showed only ATP binding domain and no other domain was observed. Further, levels of homology amongst human and bovine DExH/D RNA helicases are shown in Tables 1 and 2. Bovine DEAD helicases showed high similarity with their human counterpart (identity 76–100 %).
Fig. 6

Schematic diagrams of domain organisation in bovine DEAD helicases. Domain analysis was conducted using Scan Prosite (http://expasy.org). The domain structures were downloaded and used for figure generations. The number shown in black and red colour indicates the amino acids spanning motifs in bovine and Human DEAD box proteins

Fig. 7

Schematic diagrams of domain organisation in bovine DEAH helicases. Domain analysis was conducted using Scan Prosite (http://expasy.org). The domain structures were downloaded and used for figure generations. The number shown in black and red colour indicates the amino acids spanning motifs in bovine and Human DEAH box proteins

The higher similarity of these bovine helicases with well characterized human helicases can help to predict their functions in cattle developmental processes also. The putative functions of these helicases have been summarized in Tables 3 and 4. The importance of DExH/D RNA helicases in environmental stress is becoming evident (Shih and Lee 2014). DDX1, 3, 5, 6, 17, 21, 24, 47, DHX9 and DHX36 are associated with various viral infections. Similarly DDX6 and DDX19 are associated with neurological disorders, as summarised previously (Steimer and Klostermeier 2012). This manuscript presents first report on genome-wide comprehensive analysis of bovine DExH/D helicases providing valuable information regarding classification and putative function of these RNA helicases, essential for growth and development. Identification of bovine counterparts of helicases associated with various stress and diseases can be exploited as prognostic and diagnostic markers.
Table 3

Putative functions of DDX members

Protein

Function

Ref.

DDX1

Associated with ARE mediated mRNA decay

Chou et al. (2013)

DDX3X, DDX3Y

DDX3X can bind with DNA, RNA splicing, nuclear transport of RNA and translational regulation

Franca et al. (2007); Rosner and Rinkevich (2007)

DDX4

Bovine vasa homolog (BVH) and is expressed in gonads

Bartholomew and Parks (2007)

DDX5, DDX17

Splicing and transcriptional regulation

Auboeuf et al. (2002)

DDX6

Spermatogenesis and localized in spermatogenic cells

Kawahara et al. (2014)

DDX10

Ribosome assembly

Savitsky et al. (1996)

DDX18

Hematopoiesis and deletion resulted into p-53 depended cell arrest in G1

Payne et al. (2011)

DDX19

m-RNA nuclear transport by remodelling of RNP particles through nuclear pore complex

Collins et al. (2009)

DDX20

Transcriptional regulation, splicing process and mi-RNA pathway

Takata et al. (2012)

DDX23

Pre-mRNA splicing

Ismaïli et al. (2001)

DDX24

Innate immune signalling regulation

Ma et al. (2013)

DDX25

Posttranscriptional regulations of genes for spermatid elongation & completion of spermatogenesis

Dufau and Tsai-Morris (2007)

DDX27

ND

 

DDX28

Cellular division

Loo et al. (2012)

DDX31

Transcription of rRNA gene and assembly of 60 s ribosomal subunit

Bish and Vogel (2014)

DDX39

mRNA splicing, genome integrity and telomere protection

Yoo and Chung (2011)

DDX41

Type 1 interferon response

Zhang et al. (2011a)

DDX42

Function as chaperon

Uhlmann-Schiffler et al. (2006)

DDX43

ND

 

DDX46

Pre-mRNA splicing

Hozumi et al. (2012)

DDX47

Pre-RNA processing

Sekiguchi et al. (2006)

DDX49

ND

 

DDX51

Ribosome synthesis and formation of 3′end of 28S rRNA

Srivastava et al. (2010)

DDX52

ND

 

DDX53

ND

 

DDX54

Maintenance of central nervous system

Zhan et al. (2013)

DDX55

ND

 

DDX56

Assembly of pre-ribosomal particles

Zirwes et al. (2000)

DDX59

Pathogenesis of orofaciodigital syndrome

Shamseldin et al. (2013)

EIF4A

eIF4F complex formation and facilitates translation

Harms et al. (2014)

Nucleolar RNA Hel2 (DDX21)

RNA processing during interphase of mitosis

De Wever et al. (2012)

Table 4

Putative functions of DHX members

Protein

Function

Ref.

DHX8

Mitosis and involved in mRNA splicing

English et al. (2012)

DHX9

RNA induced silencing complex (RISC) loading factor

Fu and Yuan (2013)

DHX15

RNA virus sensing and activating immune system

Lu et al. (2014)

DHX16

Splicing

Gencheva et al. (2010)

DHX29

Protein synthesis

Pisareva et al. (2008)

DHX30

Mitochondrial DNA replication

Zhou et al. (2008)

DHX32

Lymphocyte differentiation and T cell apoptosis

Huang et al. (2009)

DHX33

rRNA transcript and nucleolar organizer

Zhang et al. (2011b)

DHX34

NMD (nonsense-mediated mRNA decay)

Anastasaki et al. (2011)

DHX35

ND

 

DHX36

Viral nucleic acid sensors, affinity towards G4-quadruplex

Fullam and Schroder (2013)

DHX37

Glycinergic synaptic transmission and associated motor behaviour

Hirata et al. (2013)

DHX38

Associated with retinitis pigmentosa

Ajmal et al. (2014)

DHX40

Pre mRNA splicing and ribosome biogenesis

Xu et al. (2002)

DHX57

ND

 

DHX58

Innate antiviral immune response

Li et al. (2009)

Conclusions

Bos taurus genome encodes 54 DExH/D family members (38 DDX and 16 DHX). Present work describes their evolutionary relationship, putative functions, pI, molecular weight and localization. Despite high similarity with well characterized counterparts, for some members, functions could not be predicted which needs further analysis. Hence, this study emphasises towards some bovine DExH/D members requiring further biological characterisation. Similarly, bovine DDX49 and DHX32 need biochemical characterization as they showed unique properties. Association analysis of these members with different abiotic and biotic stress may facilitate new diagnostic markers and drug targets.

Declarations

Authors’ contributions

MKS designed, performed experiments, analysed data and prepared manuscript; MP performed experiments; SM analysed and reviewed manuscript data; SKK supervised all experiments. All authors read and approved the final manuscript.

Acknowledgements

The present work was supported by grants from RKVY (RashtriyaKrishiVikasYojna) Bio-Informatics Project (RAJUVAS CSA-RKVY-1(11)).

Competing interests

The authors declare that they have no competing interests.

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Authors’ Affiliations

(1)
Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary & Animal Sciences

References

  1. Ajmal M, Khan MI, Neveling K, Khan YM, Azam M, Waheed NK, Hamel CP, Ben-Yosef T, De Baere E, Koenekoop RK, Collin RW, Qamar R, Cremers FP (2014) J Med Genet 51:444–448View ArticleGoogle Scholar
  2. Anastasaki C, Longman D, Capper A, Patton EE, Caceres JF (2011) Dhx34 and Nbas function in the NMD pathway and are required for embryonic development in zebrafish. Nucleic Acids Res 39:3686–3694View ArticleGoogle Scholar
  3. Auboeuf D, Honig A, Berget SM, O’Malley BW (2002) Coordinate regulation of transcription and splicing by steroid receptor coregulators. Science 298:416–419View ArticleGoogle Scholar
  4. Bartholomew RA, Parks JE (2007) Identification, localization, and sequencing of fetal bovine VASA homolog. Anim Reprod Sci 101:241–251View ArticleGoogle Scholar
  5. Bish R, Vogel C (2014) RNA binding protein-mediated post-transcriptional gene regulation in medulloblastoma. Mol Cells 37:357–364View ArticleGoogle Scholar
  6. Caruthers JM, McKay DB (2002) Helicase structure and mechanism. Curr Opin Struct Biol 12:123–133View ArticleGoogle Scholar
  7. Chou CF, Lin WJ, Lin CC, Luber CA, Godbout R, Mann M, Chen CY (2013) DEAD box protein DDX1 regulates cytoplasmic localization of KSRP. PLoS One 8:e73752View ArticleGoogle Scholar
  8. Collins R, Karlberg T, Lehtio L, Schutz P, van den Berg S, Dahlgren LG, Hammarstrom M, Weigelt J, Schuler H (2009) The DEXD/H-box RNA helicase DDX19 is regulated by an {alpha}-helical switch. J Biol Chem 284:10296–10300View ArticleGoogle Scholar
  9. Cordin O, Banroques J, Tanner NK, Linder P (2006) The DEAD-box protein family of RNA helicases. Gene 367:17–37View ArticleGoogle Scholar
  10. De Wever V, Lloyd DC, Nasa I, Nimick M, Trinkle-Mulcahy L, Gourlay R, Morrice N, Moorhead GB (2012) Isolation of human mitotic protein phosphatase complexes: identification of a complex between protein phosphatase 1 and the RNA helicase Ddx21. PLoS One 7:e39510View ArticleGoogle Scholar
  11. Dufau ML, Tsai-Morris CH (2007) Gonadotropin-regulated testicular helicase (GRTH/DDX25): an essential regulator of spermatogenesis. Trends Endocrinol Metab 18:314–320View ArticleGoogle Scholar
  12. English MA, Lei L, Blake T, Wincovitch SM Sr, Sood R, Azuma M, Hickstein D, Liu PP (2012) Incomplete splicing, cell division defects, and hematopoietic blockage in dhx8 mutant zebrafish. Dev Dyn 241:879–889View ArticleGoogle Scholar
  13. Franca R, Belfiore A, Spadari S, Maga G (2007) Human DEAD-box ATPase DDX3 shows a relaxed nucleoside substrate specificity. Proteins 67:1128–1137View ArticleGoogle Scholar
  14. Fu Q, Yuan YA (2013) Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9). Nucleic Acids Res 41:3457–3470View ArticleGoogle Scholar
  15. Fullam A, Schroder M (2013) DExD/H-box RNA helicases as mediators of anti-viral innate immunity and essential host factors for viral replication. Biochim Biophys Acta 1829:854–865View ArticleGoogle Scholar
  16. Gencheva M, Lin TY, Wu X, Yang L, Richard C, Jones M, Lin SB, Lin RJ (2010) Nuclear retention of unspliced pre-mRNAs by mutant DHX16/hPRP2, a spliceosomal DEAH-box protein. J Biol Chem 285:35624–35632View ArticleGoogle Scholar
  17. Harms U, Andreou AZ, Gubaev A, Klostermeier D (2014) eIF4B, eIF4G and RNA regulate eIF4A activity in translation initiation by modulating the eIF4A conformational cycle. Nucleic Acids Res 42:7911–7922View ArticleGoogle Scholar
  18. Hartung F, Plchova H, Puchta H (2000) Molecular characterisation of RecQ homologues in Arabidopsis thaliana. Nucleic Acids Res 28:4275–4282View ArticleGoogle Scholar
  19. Hirata H, Ogino K, Yamada K, Leacock S, Harvey RJ (2013) Defective escape behavior in DEAH-box RNA helicase mutants improved by restoring glycine receptor expression. J Neurosci 33:14638–14644View ArticleGoogle Scholar
  20. Hozumi S, Hirabayashi R, Yoshizawa A, Ogata M, Ishitani T, Tsutsumi M, Kuroiwa A, Itoh M, Kikuchi Y (2012) DEAD-box protein Ddx46 is required for the development of the digestive organs and brain in zebrafish. PLoS One 7:e33675View ArticleGoogle Scholar
  21. Huang C, Liang X, Huang R, Zhang Z (2009) Up-regulation and clinical relevance of novel helicase homologue DHX32 in colorectal cancer. J. Exp. Clin. Cancer Res 28:11View ArticleGoogle Scholar
  22. International Human Genome Sequencing C (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931–945View ArticleGoogle Scholar
  23. Ismaïli N, Sha M, Gustafson EH, Konarska MM (2001) The 100 kDa U5 snRNP protein (hPrp28p) contacts the 5′ splice site through its ATPase site. RNA 7:182–193View ArticleGoogle Scholar
  24. Kawahara C, Yokota S, Fujita H (2014) DDX6 localizes to nuage structures and the annulus of mammalian spermatogenic cells. Histochem Cell Biol 141:111–121View ArticleGoogle Scholar
  25. Lawrence P, Rieder E (2009) Identification of RNA helicase A as a new host factor in the replication cycle of foot-and-mouth disease virus. J Virol 83:11356–11366View ArticleGoogle Scholar
  26. Li X, Ranjith-Kumar CT, Brooks MT, Dharmaiah S, Herr AB, Kao C, Li P (2009) The RIG-I-like receptor LGP2 recognizes the termini of double-stranded RNA. J Biol Chem 284:13881–13891View ArticleGoogle Scholar
  27. Linder P (2006) Dead-box proteins: a family affair–active and passive players in RNP-remodeling. Nucleic Acids Res 34:4168–4180View ArticleGoogle Scholar
  28. Linder P, Daugeron MC (2000) Are DEAD-box proteins becoming respectable helicases? Nat Struct Biol 7:97–99View ArticleGoogle Scholar
  29. Loo LW, Cheng I, Tiirikainen M, Lum-Jones A, Seifried A, Dunklee LM, Church JM, Gryfe R, Weisenberger DJ, Haile RW, Gallinger S, Duggan DJ, Thibodeau SN, Casey G, Le Marchand L (2012) cis-Expression QTL analysis of established colorectal cancer risk variants in colon tumors and adjacent normal tissue. PLoS One 7:e30477View ArticleGoogle Scholar
  30. Lu H, Lu N, Weng L, Yuan B, Liu YJ, Zhang Z (2014) DHX15 senses double-stranded RNA in myeloid dendritic cells. J Immunol 193:1364–1372View ArticleGoogle Scholar
  31. Ma Z, Moore R, Xu X, Barber GN (2013) DDX24 negatively regulates cytosolic RNA-mediated innate immune signaling. PLoS Pathog 9:e1003721View ArticleGoogle Scholar
  32. Murphy WJ, Pevzner PA, O’Brien SJ (2004) Mammalian phylogenomics comes of age. Trends Genet 20:631–639View ArticleGoogle Scholar
  33. Patel SS, Donmez I (2006) Mechanisms of helicases. J Biol Chem 281:18265–18268View ArticleGoogle Scholar
  34. Payne EM, Bolli N, Rhodes J, Abdel-Wahab OI, Levine R, Hedvat CV, Stone R, Khanna-Gupta A, Sun H, Kanki JP, Gazda HT, Beggs AH, Cotter FE, Look AT (2011) Ddx18 is essential for cell-cycle progression in zebrafish hematopoietic cells and is mutated in human AML. Blood 118:903–915View ArticleGoogle Scholar
  35. Pisareva VP, Pisarev AV, Komar AA, Hellen CU, Pestova TV (2008) Translation initiation on mammalian mRNAs with structured 5′UTRs requires DExH-box protein DHX29. Cell 135:1237–1250View ArticleGoogle Scholar
  36. Pyle AM (2008) Translocation and unwinding mechanisms of RNA and DNA helicases. Annu Rev Biophys 37:317–336View ArticleGoogle Scholar
  37. Radi M, Falchi F, Garbelli A, Samuele A, Bernardo V, Paolucci S, Baldanti F, Schenone S, Manetti F, Maga G, Botta M (2012) Discovery of the first small molecule inhibitor of human DDX3 specifically designed to target the RNA binding site: towards the next generation HIV-1 inhibitors. Bioorg Med Chem Lett 22:2094–2098View ArticleGoogle Scholar
  38. Rosner A, Rinkevich B (2007) The DDX3 subfamily of the DEAD box helicases: divergent roles as unveiled by studying different organisms and in vitro assays. Curr Med Chem 14:2517–2525View ArticleGoogle Scholar
  39. Savitsky K, Ziv Y, Bar-Shira A, Gilad S, Tagle DA, Smith S, Uziel T, Sfez S, Nahmias J, Sartiel A, Eddy RL, Shows TB, Collins FS, Shiloh Y, Rotman G (1996) A human gene (DDX10) encoding a putative DEAD-box RNA helicase at 11q22-q23. Genomics 33:199–206View ArticleGoogle Scholar
  40. Sekiguchi T, Hayano T, Yanagida M, Takahashi N, Nishimoto T (2006) NOP132 is required for proper nucleolus localization of DEAD-box RNA helicase DDX47. Nucleic Acids Res 34:4593–4608View ArticleGoogle Scholar
  41. Shamseldin HE, Rajab A, Alhashem A, Shaheen R, Al-Shidi T, Alamro R, Al Harassi S, Alkuraya FS (2013) Mutations in DDX59 implicate RNA helicase in the pathogenesis of orofaciodigital syndrome. Am J Hum Genet 93:555–560View ArticleGoogle Scholar
  42. Shih J, Lee YW (2014) Human DExD/H RNA helicases: emerging roles in stress survival regulation. Clin Chim Acta 436:45–58View ArticleGoogle Scholar
  43. Srivastava L, Lapik YR, Wang M, Pestov DG (2010) Mammalian DEAD box protein Ddx51 acts in 3′ end maturation of 28S rRNA by promoting the release of U8 snoRNA. Mol Cell Biol 30:2947–2956View ArticleGoogle Scholar
  44. Staley JP, Guthrie C (1998) Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92:315–326View ArticleGoogle Scholar
  45. Steimer L, Klostermeier D (2012) RNA helicases in infection and disease. RNA Biol 9:751–771View ArticleGoogle Scholar
  46. Svitkin YV, Pause A, Haghighat A, Pyronnet S, Witherell G, Belsham GJ, Sonenberg N (2001) The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 5′ secondary structure. RNA 7:382–394View ArticleGoogle Scholar
  47. Takata A, Otsuka M, Yoshikawa T, Kishikawa T, Kudo Y, Goto T, Yoshida H, Koike K (2012) A miRNA machinery component DDX20 controls NF-κB via microRNA-140 function. Biochem Biophys Res Commun 420:564–569View ArticleGoogle Scholar
  48. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739View ArticleGoogle Scholar
  49. Tanner NK, Linder P (2001) DExD/H box RNA helicases: from generic motors to specific dissociation functions. Mol Cell 8:251–262View ArticleGoogle Scholar
  50. Tanner NK, Cordin O, Banroques J, Doere M, Linder P (2003) The Q motif: a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis. Mol Cell 11:127–138View ArticleGoogle Scholar
  51. The Bovine Genome Sequencing and Analysis Consortium (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522–528View ArticleGoogle Scholar
  52. Tuteja N, Tuteja R (2004a) Prokaryotic and eukaryotic DNA helicases. Essential molecular motor proteins for cellular machinery. Eur J Biochem 271:1835–1848View ArticleGoogle Scholar
  53. Tuteja N, Tuteja R (2004b) Unraveling DNA helicases. Motif, structure, mechanism and function. Eur J Biochem 271:1849–1863View ArticleGoogle Scholar
  54. Uhlmann-Schiffler H, Jalal C, Stahl H (2006) Ddx42p–a human DEAD box protein with RNA chaperone activities. Nucleic Acids Res 34:10–22View ArticleGoogle Scholar
  55. Umate P, Tuteja N, Tuteja R (2011) Genome-wide comprehensive analysis of human helicases. Commun Integr Biol 4:118–137View ArticleGoogle Scholar
  56. Xu J, Wu H, Zhang C, Cao Y, Wang L, Zeng L, Ye X, Wu Q, Dai J, Xie Y, Mao Y (2002) Identification of a novel human DDX40 gene, a new member of the DEAH-box protein family. J Hum Genet 47:681–683View ArticleGoogle Scholar
  57. Xu R, Zhang S, Huang J, Zheng C (2013) Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparision with Arabidopsis and Oryza sativa. PLoS One 8:e78982View ArticleGoogle Scholar
  58. Yoo HH, Chung IK (2011) Requirement of DDX39 DEAD box RNA helicase for genome integrity and telomere protection. Aging Cell 10:557–571View ArticleGoogle Scholar
  59. Zhan R, Yamamoto M, Ueki T, Yoshioka N, Tanaka K, Morisaki H, Seiwa C, Yamamoto Y, Kawano H, Tsuruo Y, Watanabe K, Asou H, Aiso S (2013) A DEAD-box RNA helicase Ddx54 protein in oligodendrocytes is indispensable for myelination in the central nervous system. J Neurosci Res 91:335–348View ArticleGoogle Scholar
  60. Zhang Z, Yuan B, Bao M, Lu N, Kim T, Liu YJ (2011a) The helicase DDX41 senses intracellular DNA mediated by the adaptor STING in dendritic cells. Nat Immunol 12:959–965View ArticleGoogle Scholar
  61. Zhang Y, Forys JT, Miceli AP, Gwinn AS, Weber JD (2011b) Identification of DHX33 as a mediator of rRNA synthesis and cell growth. Mol Cell Biol 31:4676–4691View ArticleGoogle Scholar
  62. Zhou Y, Ma J, Bushan Roy B, Wu JY, Pan Q, Rong L, Liang C (2008) The packaging of human immunodeficiency virus type 1 RNA is restricted by overexpression of an RNA helicase DHX30. Virology 372:97–106View ArticleGoogle Scholar
  63. Zirwes RF, Eilbracht J, Kneissel S, Schmidt-Zachmann MS (2000) A novel helicase-type protein in the nucleolus: protein NOH61. Mol Biol Cell 11:1153–1167View ArticleGoogle Scholar

Copyright

© Suthar et al. 2016