Journal of ISSN: 2377-4312JDVAR

Dairy, Veterinary & Animal Research
Research Article
Volume 4 Issue 3 - 2016
Sequence Length Variation and Transmembrane Analysis of Contagious Bovine Pleuropneumonia (CBPP) and Contagious Caprine Pleuropneumonia (CCPP) Proteins
Dauda A1, Abbaya HY2, Malgwi IH3*, and Abare EA4
1Department of Animal Science, University of Agriculture, Nigeria
2Department of Animal Science, Adamawa State University, Nigeria
3Department of Animal Science, University of Maiduguri, Nigeria
4Department of Animal Science, Ahmad Bello University, Nigeria
Received: October 18, 2016 | Published: December 08, 2016
*Corresponding author: IH Malgwi, Department of Animal Science, University of Maiduguri, PMB 1069. Borno State, Nigeria, Email:
Citation: Dauda A, Abbaya HY, Malgwi IH, Abare EA (2016) Sequence Length Variation and Transmembrane Analysis of Contagious Bovine Pleuropneumonia (CBPP) and Contagious Caprine Pleuropneumonia (CCPP) Proteins. J Dairy Vet Anim Res 4(3): 00121. DOI: 10.15406/jdvar.2016.04.00121

Abstract

A total of forty (40) contagious bovine pleuropneumonia (CBPP) and contagious caprine pleuropneumonia (CCPP) proteins comprising 20 each of cattle and goats were retrieved from the GenBank (www.ncbi.nlm.nih.gov). The Genbank accession numbers of the sequences and sequence variations of the proteins were used to investigate the molecular identity of various CBPP and CCPP proteins. The protein molecules of the CBPP and CCPP proteins had varied amino acid sequences. This indicated that the genome that coded for the building of their protein molecule exhibited high level of polymorphism. The CBPP and CCPP protein’s amino acid sequences were subjected to transmembrane domain identification using TMbase. The Transmembrane of CBPP revealed that the inside to outside and outside to inside are significant while that of CCPP inside to outside only sequence position from 354-370 is significant and outside to inside only sequence position from 353-370 is significant. Phylogenetic trees analysis by Neighbor-Joining (NJ) trees were constructed using CBPP and CCPP protein sequences. The evolutionary distances were computed using the Poisson correction method. The reliability of the trees was calculated by bootstrap confidence values with 1000 bootstrap iterations using MEGA 5.1 software. Similar CBPP and CCPP proteins tend to cluster together compared to proteins that are distantly related in both species. This could be seen among others in the closeness of protein P62415-Phosphoglycerate kinase-bovine and KEY84661-Phosphoglycerate kinase-caprine. The study concluded that new typing tool may help improve the surveillance and control of the disease, as well as to trace new epidemics.

Keywords: Bovine; Caprine; Pleuropneumonia; Proteins; Sequence; Transmembrane

Introduction

Contagious bovine pleuropneumonia (CBPP) is an infectious disease of cattle caused by the small-colony type of mycoplasma mycoides subspecies mycoides [1]. The Pan African Programme for the Control of Epizootics (PACE) (this programme is implemented by the African Union Inter-African Bureau for Animal Resources [AU-IBAR] in 32 African countries and is funded principally by the European Commission with the support of the participating African countries) has identified CBPP as the second most important transboundary disease in Africa after rinderpest [2]. Transmission occurs from direct and repeated contact between sick and healthy animals. The first incidence of the disease in Nigeria was recorded in 1924 when reliable records were first available [3].

Contagious Caprine Pleuropneumonia (CCPP) is a devastating disease of goats cause by infectious agent Mycoplasma capricoleum subspecies capripneumoniae, formerly known as the F38-like group, is difficult to isolate and has only been identified in a few of the countries where the disease has been reported [4]. CCPP occurs in per acute, acute or chronic forms and is characterized by fibrinous pneumonia, pleurisy and profuse pleural exudates. Mortality rates of 60–100% are common [5]. The aim of this study is to determine the sequence length variation, transmembrane and phylogenic analysis of CBPP and CCPP proteins.

Materials and Methods

A total of forty (40) CBPP and CCPP proteins comprising 20 each of cattle and goats were retrieved from the GenBank (www.ncbi.nlm.nih.gov). The Genbank accession numbers for CBPP are AAU26106, Q6MTR9, Q6MTG9, P62415, NP975936-IS 1634BQ, ADK70040, CAL91969, CAE76667, CAE76666, Q6MRX5, NP975877, CAE76664, NP975938, AAUI4997, Q6MS92, NP975087, CAE76665, YP00781134, NP975898, Q6MUE3 and for CCPP are KEY8461, KEY84219, KEY84758, KEY84567, KEY84560, KEY84622, KEY84568, KEY84179, KEY84763, KEY84755, KEY84779, KEY84654, KEY84580, KEY84577, KEY84753, KEY84440, KEY84751, KEY84561, KEY84539, KEY84596. Sequences alignment and comparison were done with Clustal W as described by Larkin et al. [6] using IUB substitution matrix, gap open penalty of 15 and gap extension penalty of 6.66. The prediction of transmembrane domain of CBPP and CCPP proteins cattle and goats were also subjected to transmembrane domain identification using TMbase - A Database of Membrane Spanning Protein Segments [7]. TMbase is mainly based on SwissProt, but contains information from other sources as well. Phylogenetic trees analysis by Neighbor-Joining (NJ) trees were constructed using CBPP and CCPP protein sequences. The evolutionary distances were computed using the Poisson correction method. The reliability of the trees was calculated by bootstrap confidence values [8], with 1000 bootstrap iterations using MEGA 5.1 software [9].

Results

The variation in sequence length in base pair (bp) of CBPP protein ranges between 334bp and 1255bp (Table 1). The variation in sequence length in base pair (bp) of CCPP protein ranges between 364bp and 988bp (Table 2). Prediction of transmembrane helices of amino acid permease-bovine (NP975877) of cattle indicated twelve inside to outside helices and twelve outside to inside helices (Tables 3 & 4). The prediction plot is shown in Figure 1 with varying topologies of the transmembrane segments. Prediction of transmembrane helices of phosphoglycerate kinase-caprine (KEY8461) of goat indicated three inside to outside helices and three outside to inside helices (Tables 5 & 6). The prediction plot is shown in Figure 2 with varying topologies of the transmembrane segments. Figure 3 shows phylogenetic tree-like pattern used in describing the evolutionary relationships between the CBPP and CCPP proteins. Similar CBPP and CCPP proteins tend to cluster together compared to proteins that are distantly related in both species. This could be seen among others in the closeness of protein P62415-Phosphoglycerate kinase-bovine and KEY84661-Phosphoglycerate kinase-caprine.

Accession Number

Base Pair Number

Sequence length variation

AAU26106

622

334 – 1255

Q6MTR9

474

 

Q6MTG9

433

 

P62415

404

 

NP975936-IS 1634BQ

557

 

ADK70040

557

 

CAL91969

470

 

CAE76667

532

 

CAE76666

548

 

Q6MRX5

1255

 

NP975877

512

 

CAE76664

550

 

NP975938

334

 

AAUI4997

622

 

Q6MS92

525

 

NP975087

911

 

CAE76665

549

 

YP00781134

406

 

NP975898

643

 

Q6MUE3

944

 

Table 1: Accession Number and Sequence Length Variation of CBPP protein.

Accession Number

Base Pair Number

Sequence Length Variation

KEY8461

404

364 – 988

KEY84219

372

 

KEY84758

515

 

KEY84567

456

 

KEY84560

754

 

KEY84622

779

 

KEY84568

604

 

KEY84179

414

 

KEY84763

364

 

KEY84755

665

 

KEY84779

452

 

KEY84654

414

 

KEY84580

602

 

KEY84577

820

 

KEY84753

369

 

KEY84440

500

 

KEY84751

526

 

KEY84561

988

 

KEY84539

424

 

KEY84596

447

 

Table 2: Accession Number and Sequence Length Variation of CCPP protein.

Sequence Position

From

To

Score

7

26

1855

44

62

2331

97

115

1234

128

144

2635

162

179

1673

209

228

1249

242

258

2079

295

315

2337

345

364

2241

394

413

1897

433

449

2819

473

489

2650

Table 3: Inside to outside helices of cattle transmembrane amino acid-permease-bovine.

Significant for any score above 500

Sequence Position

From

To

Score

10

26

1707

41

59

2493

99

117

1209

129

147

2930

159

176

1693

210

228

1944

242

258

2188

297

314

2420

349

367

2168

391

413

1999

432

452

2430

473

490

2924

Table 4: Outside to inside helices of cattle transmembrane amino acid permease-bovine.

Significant for any score above 500

Sequence Position

From

To

Score

166

182

369

354

370

682

366

383

143

Table 5: Inside to outside helices of goat transmembrane phosphoglycerate_kinase-caprine.

Significant for any score above 500

Sequence Position

From

To

Score

40

60

11

166

184

462

353

370

529

Table 6: Outside to inside helices of cattle transmembrane phosphoglycerate_kinase-caprine.

Significant for any score above 500

Figure 1: Prediction plot of transmembrane topology of cattle amino acid_permease bovine.
io: inside to outside; oi: the opposite
inside' means normally the cytoplasmic face
outside' the lumenal face of the membrane depending on the organelle
Figure 2: Prediction plot of transmembrane topology of goat phosphoglycerate_kinase-caprine.
io: inside to outside; oi:the opposite
inside' means normally the cytoplasmic face
outside' the lumenal face of the membrane depending on the organelle
Figure 3: Evolutionary relationships of CBPP and CCPP proteins.

Discussion

The variation in sequence length within and among species might results from evolution and differentiation [10]. There are cases where variability might results from DNA duplication, DNA rearrangement, short tandem repeat (STR), insertions or deletion of sequences [11]. The length variation observed within and across species in this study might be due to differences in the genomic region where the sequences were obtained from and differences due to complete coding or partial coding. In CBPP and CCPP proteins, the sequences are partial coding sequences (CDS) from DNA and had sequence length that are less than six thousand base pair (<6000bp). This variability might initiate unique structures between individual members in conferring different biological activities. Many important biological processes such as cell signaling, transport of membrane-impermeable molecules, cell–cell communication, cell recognition and cell adhesion are mediated by membrane proteins [12]. Although there has been some recent progress in predicting the full 3-D structure of transmembrane proteins (e.g. Yarov-Yarovoy et al. [13]), the most widely applied prediction technique for these proteins is to determine the transmembrane topology, i.e. the inside–outside location of the N and C terminal relative to the cytoplasm, along with the number and sequence locations of the membrane spanning regions. This will facilitate the understanding of the structure and function of CBPP and CCPP proteins. The genetic relationships of the proteins of CBPP and CCPP as revealed by the phylogenetic tree were in accordance with the well-known evolutionary history of Bovidae subfamily speciation [14]. The implication of the similarities in the proteins of CBPP and CCPP is that if vaccine and therapeutic is prepare for CBPP might also be effective for CCPP. Genetic data may bring new insights into epidemiological questions. Molecular typing has been instrumental in determining the population structure and evolution of pathogens. Since CBPP and CCPP has both economical and nutritional consequences, efforts should be intensified towards finding sustainable genomic solutions to these deadly diseases which continue to ravage the livestock industry.

Conclusion

This study revealed that, there is sequence variation within and between species. The sequence length for both CBPP and CCPP proteins indicated partial coding. The transmembrane of CBPP is significant from inside to outside and outside to inside while the CCPP is significant at only one sequence position. The genetic relationship of CBPP and CCPP proteins shows similarities. New typing tool may help improve the surveillance and control of the disease, as well as to trace new epidemics.

References

  1. Masiga WN, Domenech J (1995) Overview and epidemiology of contagious bovine pleuropneumonia in Africa. Rev Sci Tech 14(3): 611-630.
  2. Tambi NE, Maina WO, Ndi C (2006) An estimation of the economic impact of contagious bovine pleuropneumonia in Africa. Rev Sci Tech 25(3): 999-1012.
  3. Faluso EF (2004) Status of contagious bovine pleuropneumonia in Nigeria with emphasis on control stretagies. Proceeding of the FAO-OIE-AU/IBAR-IAEA consultative Group on CBPP 3rd meeting, Toward sustainable CBPP control programmes in Africa, Nov 12-14, 2003, Rome, p: 2-46.
  4. Bölske G, Johansson KE, Heinonen R, Panvuga PA, Twinamasiko E (1995) Contagious caprine pleuropneumonia in Uganda and isolation of Mycoplasma capricolum subspecies capripneumoniae from goats and sheep. Vet Rec 137(23): 594.
  5. Edelsten RM, Gourlay RN, Lawson GKH, Morrow AN, Ramachandran S (1990) Diseases caused by bacteria. In: Sewell MMH & Brocklesby DW (Eds), Handbook on animal diseases in the tropics. Baillière Tindall, London, UK.
  6. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21): 2947-2948.
  7. Hofmann K, Stoffel W (1993) TMbase - A database of membrane spanning proteins segments. Biol Chem Hoppe-Seyler 347: 166.
  8. Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39(4): 783-791.
  9. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA 5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28(10): 2731-2739.
  10. Yakubu A, Alade ED, Dim NI (2014) Molecular analysis of Solute Carrier Family 11 A1 (SLC11A1) gene in ruminants and non-ruminants using computational method. Genetika 46(3): 925-934.
  11. Vincent ST, Momoh OM, Yakubu A (2014) Bioinformatics analysis of beta-casein gene in some selected mammalian species. Research Opinions in Animal and Veterinary Sciences 4(10): 564-570.
  12. Jones DT (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23(5): 538-544.
  13. Yarov-Yarovoy V, Schonbrun J, Baker D (2006) Multipass membrane protein structure prediction using Rosetta. Proteins 62(4): 1010-1025.
  14. Floudas CA (2007) Computational methods in protein structure prediction. Biotechnology and Bioengineering 97(2): 207-213.
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