Functional Annotation and Molecular modeling of Hypothetical Proteins (HPs) from P.aeruginosa plasmid pUM505: An In silico Approach

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Functional Annotation and Molecular modeling of Hypothetical Proteins (HPs) from P.aeruginosa plasmid pUM505: An In silico Approach

Srikant Awasthi1-2, Pragya Saxena2, Hillol Chakdar2, Alok K Srivastava2 and Salman Akhtar1*

1Department of Bioengineering, Integral University, Lucknow, INDIA, 226026

2Microbial Genomics Laboratory, National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, INDIA, 275101

Dr. Salman Akhtar Associate Professor

Department of Bioengineering Integral University, Lucknow, India 226026

Abstract:- Structural and function annotation of P. aeruginosa plasmid pUM505isessentially required to facilitate the understanding of mechanisms of pathogenesis and biochemical pathways important for selecting novel therapeutic target. In present study, randomly selected twelve hypothetical protein sequence of P. aeruginosa plasmid pUM505 has been annotated using various In-Silico tools and databases to determine domain family, solubility of protein, ligand binding sites etc. Six out of 12 proteins have been putatively annotated, in which four have been annotated with high confidence. Physio-chemical characterization revealed two proteins are stable. The three-dimensional structure of two important annotated proteins were modeled and their ligand binding sites were identified. Domains and families for six proteins have been found. The analysis revealed that these proteins have antitoxin activity, integrase enzyme activity, conjugal DNA transfer activity, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against various diseases.

Keywords: Hypothetical Protein, Functional Annotation, Molecular Modeling, Docking

  1. INTRODUCTION

    Pseudomonas aeruginosa, a gram-negative bacteriumis well known for its environmental versatility. Diverse growing habitat includes soil,coastal marine, plant and animal tissues (Khan et al., 2007). P. aeruginosais also well known for its multidrug resistant and is a global threat towards many infections disease. P. aeruginosais a major opportunistic pathogen in humans, causing serious complications caused by infections in patients particularly susceptible like people with immune system deficiencies, victims of skin burns, catheterized patients who suffer urinary tract infections and patients with respirators, causing nosocomial pneumonia (Lyczak et al., 2000). It is the major cause of mortality in patients with cystic fibrosis colonizing the lungs (Williams et al., 2010). Role of plasmids in antibiotic resistance are well establish.Plasmids are circular deoxyribonucleic acid molecules that exist in bacteria, usually independent of the chromosome. The study of plasmids is important to medical microbiology because plasmids can encode genes for antibiotic resistance or virulence factors (Wang et al., 1988). The pUM505 plasmid contains a genomic island with sequence similar to islands found in chromosomes of virulent P. aeruginosa clinical isolates. Plasmid pUM505 contains several genes that encode virulence factors, suggesting that the plasmid may contribute directly to bacterial virulence (Rodríguezetal., 2016). The bacterium's virulence depends on a large number of cell-associated and extracellular factors. The virulence factors play an important pathological role in the colonization, the survival of the bacteria and the invasion of tissues(Wang and Gui, 2013).

    Due to cost-efficiency throughput of genome sequencing has increased enormously resulting thousands of bacterial genomes now available and this number is increasing enormously day by day.Functional annotation of proteomes is a demanding problem(Roberts et al., 2004). A large fraction of proteins is still labeled as hypothetical protein,unknownfunction or with similar terms that imply that there is no functional indication for the ORF.Function annotation of putative uncharacterized HPs for their possible biological activity has emerged as an important focus for computational biology (Kumar et al., 2014; Loewenstein et al., 2009; Shahbaaz et al., 2013).The pUM505 sequence contained 138 complete coding regions, the majority of them encoded on the complementary DNA strand (75%), with respect to the predicted origin of replication (oriV). Most of the identified genes (46%) encode hypothetical proteins (HSPs). Proper structural and functional determination of this huge fraction (46%) is very important to reveal complete understanding of virulence mechanism in P. aeruginosa.Therefor an improved functional annotation of its proteome is of particular urgency. In present study, 12 randomly selected HPs from P.aeruginosa plasmid pUM505 have been annotated with the help of various bioinformatics resources. Moreover, two important annotated HPS have been structurally modeled and characterized.

  2. MATERIALS AND METHODS

      1. Sequence retrieval and physiochemical characterization

        Randomly selected twelve HPs which contain standard number of amino acids sequences of P.aeruginosa plasmid pUM505 were retrieved from NCBI (http://www.ncbi.nlm.nih.gov/).For Physio-chemical characterization EXPAXY ProtParam (Gasteigeret al.,2005) tool were used.

      2. Functional characterization

        Functional annotation was performed using conserved domain database (CDD) (MarchlerBauer et al. 2011)Pfam (Bateman et al.,2005) and EGGNOG (Powell et al., 2012).CELLO (Yu et al., 2014) and PSORT B (Gardyet. al., 2003)were used for subcellular localization of proteins. Signal Peptide(Yuet al., 2010)and SecretomePwere used for nonclassicalsecretory pathway in proteins.

      3. 3D structure modelling

        Homology models of HPs were determined using SWISSMODEL (Kieferet al.,2009) and protein homology recognition engine Phyre2 (Kelley and Sternberg,2009).The Phyre server uses a library of known protein structures taken from the structural classification of proteins (SCOP) database and the PDB (Kelley and Sternberg 2009). The top ten scoring alignments were used to construct the three-dimensional structure of each HP.

      4. Validation of predicted model

        The stereo-chemical quality of the modeled structure for HPs was validated with verification server PDBSUM (Laskowski et al., 1993) using PROCHECK (Laskowski et al., 1996). PROCHECK validates the stereochemical quality of a protein structure by analyzing the overall structure and residue-by-residue geometry of proteins. ERRAT server (Li et al., 2007) was used for structure validation.

      5. Active site prediction

    MetaPocket 2.0(http://projects.biotec.tu-dresden.de/metapocket/help.php)was used to find out the ligand binding sites.Proteins are primarily scanned for ligands and it uses the interaction energy between the protein and a simple van der Waals probe to locate vigorously favorable binding sites (Zhang et al., 2011).

  3. RESULTS AND DISCUSSION

      1. Sequence analysis and functional annotation

        Physicochemical studies of selected proteins revealed that two out of 12 proteins are stable. Most of the proteins are of acidic in nature (Supplementary Table S1).In pursuit of assigning putative function to hypotheticalproteins,available sequences and functional information from various resources has been interrogated. Six out of 12 selected hypothetical proteins have been putatively annotated usingsequence/domaininformationfromPFAM,functionalinformationfromEGGNOG,pathway(Table1).The presence of different domains in varying combinations in different proteins gives rise to th diverse repertoire of proteins found in nature. Identifying the domains present in a protein can provide insights into the function of that protein.Protein YP_004928038.1 has been annotated as PIN3 family protein,YP_004928003.1 asTraU family,YP_004927980.1 as NA-37 family, and YP_004927989.1 as HNH endonuclease (Table 1). Four proteins have been annotated with high confidant. PIN3 family protein plays avery important role and function as nuclease enzymes that cleave single stranded RNA in a sequence dependent manner. PIN domain contain three nearly invariant acidic residues. PIN-domain proteins found in prokaryotes are the toxic components of toxin-antitoxin operons. These loci provide a control mechanism that helps free-living prokaryotes cope with nutritional stress (Arcuset al., 2011). HNH proteins are involved in DNA homing, restriction, repair, or chromosome degradation.The HNH proteins are not only involved in homing but also carry other biological functions, such as DNA degradation, repair, and restriction (Walker et al., 2002). TraU is anessential protein to conjugal DNA transfer (Moore et al., 1990).All these annotated HPs play crucial role.Sub-cellular localization of protein is an important parameter for protein function in various cellular processes. Sub-cellular localization analysis revealed that 9 proteins are cytoplasmic, one outer membrane protein and two unknown (Table 2).Motifs are signatures of protein families and can be preferably used to define the protein function, particularly in enzyme where motifs are associated with the catalytic function (Bork and Koonin, 1996).

      2. 3D Structure prediction and Validation

        Three dimensional structures of two important annotated proteins have been done with the SWISS Model and Phyre2 server. Based on the results, the stereo chemical evaluation of backbone and dihedral angles of the HSPs revealed that for model HP38; 94.6, and5.4 % residues were within the most favored regions, additionally allowed regions respectively (Fig 1b). No residue was found in generouslyallowed or disallowedregions.For model HP80,84.6,12.8, 1.7 and 0.9% residues fallwithin the most favored regions, additionally allowed regions, generously allowed regions and disallowed regions respectively (Fig 2b).Overall 100 % implies beststereo-chemical quality for both the model. Based on the stereo chemical validation model HP38 showed more robust model than HP80.Secondary structure prediction showed 5 helices, 2 strands, 7 beta turns for model HP03 while 7 helices, 4 strands and 7 beta turns for HP38(Fig 3 a-b).

        ERRAT is a program for verifying protein structures determined by crystallography. ERRAT server was also used for model quality estimation which showed that overall quality factor was 77.11 and 81.32 % for model HP38 andHP80 respectively which confirms as a good model (Fig.1a- 2a).

      3. Active sites in predicted models

        Activesites on a protein is of fundamental importance for a range of applications including molecular docking, de novo drug design and structural identification and comparison of functional sites.During analysis, seven and four binding pockets were

        identified for model HP38 and HP80, respectively (Fig 4). During analysis of NABPs in HP38 model, two largest positive patches were detected viz Patch 1:'GHE', 'SFN', 'LCS', 'FPK', 'PAS', 'CON' Patch 2: 'FPK', 'PAS', 'LCS', 'CON', 'GHE'. For model HP38, two largest positive patches were detected viz Patcp 'GHE', 'SFN', 'LCS', 'FPK', 'PAS', 'CON' Patch 2: 'PAS','FPK', 'LCS','SFN', 'GHE' Patch 3: 'PAS', 'LCS', 'GHE'.Results are shown in Table 3. This data of active binding site residues will give insight into identifying binding interactions and docking with specific ligands.

  4. CONCLUSIONS

Our primary sequence-based analysis led to the identification of two HPs as biologically significant, which might be involved as enzymes (antitoxins, conjugal DNA transferase, and oxido-reductase etc.). Furthermore, we successfully predicted the structure of two HPs to describe their functions at the molecular level. The outcome of the present study may facilitate better understanding of the mechanism of virulence, drug resistance, pathogenesis, adaptability to host, tolerance for host immune response and drug discovery for treatment of infections caused by P. aeruginosa.

ACKNOWLEDGEMENTS

The authors gratefully acknowledge the financial assistance under project Application of Microorganisms in Agriculture and Allied Sectors (AMAAS) from Indian Council of Agricultural Research (ICAR), India. The authors further acknowledge the Integral University, Lucknow for providing the necessary support for the completion of this study and allotting its manuscript communication ID.

Conflict of interest: The authors declare that they have no conflict of interest.

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        FIGURE LEGENDS

        Fig1. (a-b) (a)Three-dimensional structure of HP38 model and (b) their stereo-chemical property by Ramchandran plot. All the residues are in most favored region

        Fig2 (a-b)(a)Three-dimensional structure of HP80 model and (b) their stereo-chemical propertyby Ramachandran plot. All the residues are in most favored region

        Fig. 3 (a-b)The secondary structure of (a) HP38 and (b) HP80 showing helices, b-Sheets and b-hairpins. Fig. 4 (a-b)Model quality estimation plot obtained by ERRAT server for (a) model HP38 and (b) model HP80. Fig4(c-d).Active sites (shown in balls) identified in protein (c) HP38 and (d) HP80.

        Fig1. (a-b):- (a)Three dimensional structure of HP38 model and (b) their stereo-chemical property by Ramchandran plot. All the residues are in most favored reg

        1. (b)

Fig2 (a-b):-(a)Three dimensional structure of HP80 model and (b) their stereo-chemical propertyby Ramachandran plot.

Fig. 3 (a-b)The secondary structure of (a) HP38 and (b) HP80 showing helices, b-Sheets and b-hairpins.

  1. (b)

    Fig. 4 (a-b):-Model quality estimation plot obtained by ERRAT server for (a) model HP38 and (b) model HP80

    1. (b)

Fig4(c-d).Active sites (shown in balls) identified in protein (c) HP38 and (d) HP80

(c) (d)

Tables

Table1. Predicted Functions of HPs in P.aeruginosa plasmid pUM505

S.No.

GenBank ID

Functional Annotation

EGGNOG

Pfam

1.

YP_004927991.1

Function Unknown

Not found

2.

YP_004928098.1

No Ortholog

Not found

3.

YP_004927980.1

Nucleoid-associated protein

NA-37 family

4.

YP_004928038.1

PIN3 domain protein

PIN3 family

5.

YP_004928012.1

Secreted protein

DUF2895

6.

YP_004927986.1

No Ortholog

Not found

7.

YP_004927975.1

Function Unknown

Not found

8.

YP_004927989.1

phage protein

HNH endonuclease

9.

YP_004928003.1

TraU

TraU family

1

YP_004928109.1

Function Unknown

DUF 1845 (family of unknown function)

1

YP_004927994.1

No Ortholog

Not found

1

YP_004928060.1

Function Unknown

DUF 1302 (family of unknown function)

Table2.Subcellular localization of HPs predicted by different bioinformatics tool

S.No

GeneBank ID

Sub-cellular localization

SignalPeptide

Secretory Protein

PSORT B

PSLpred

CELLO

1

YP_004927991.1

Cytoplasmic

Cytoplasmic protein

Cytoplasmic

No

No

2

YP_004928098.1

Cytoplasmic

Cytoplasmic protein

Cytoplasmic

No

No

3

YP_004928060.1

Outer membrane

Inner membrane protein

Outer membrane

Yes

No

4

YP_004928038.1

Cytoplasmic

Cytoplasmic protein

Cytoplasmic

No

No

5

YP_004927994.1

Cytoplasmic

Periplasmic protein

Cytoplasmic

No

No

6

YP_004927986.1

Unknown

Cytoplasmic

Cytoplasmic

No

No

7

YP_004927980.1

Cytoplasmic

Inner membrane protein

Cytoplasmic

No

No

8

YP_004927975.1

Cytoplasmic

Inner membrane protein

Cytoplasmic

No

Yes

9

YP_004927989.1

Cytoplasmic

Cytoplasmic protein

Cytoplasmic

No

No

10

YP_004928003.1

Unknown

Cytoplasmic protein

Extracellular

Yes

Yes

11

YP_004928012.1

Cytoplasmic

Inner-membrane protein

Cytoplasmic

No

No

12

YP_004928109.1

Cytoplasmic

Inner membrane protein

Cytoplasmic

No

No

Table 3. MetaPocket clusters and their unctional residues

HP Model

Pocket No.

z-score

Pocket Sites

HP38 (YP_004928038.1)

1

11.99

'GHE-1', 'SFN-1', 'LCS-1', 'FPK-1', 'PAS-2', 'CON-1'

2

3.52

'PAS-1', 'GHE-2'

3

1.49

'LCS-2'

4

0.93

'FPK-2', 'PAS-3', 'LCS-3', 'CON-2', 'GHE-3'

5

0.74

'FPK-3'

6

0.18

'SFN-2'

7

0.04

'SFN-3'

HP80 (YP_004927980.1)

1

18.38

'GHE-1', 'SFN-1', 'LCS-1', 'FPK-1', 'PAS-1', 'CON-1'

2

4.56

'PAS-2','FPK-2', 'LCS-2','SFN-2', 'GHE-2'

3

1.49

'FPK-3', 'SFN-3'

4

-0.02

'PAS-3', 'LCS-3', 'GHE-3'

Supplementary Tables

Table 1. Supplementary table S1.Physiochemical characterization of HPs protein

S.No.

Gene bank Accession Number

Sequence length

M. wt

pI

R

+ R

EC

II

Protein Claas

AI

GRAVY

1.

YP_004927991.1

228

24996.02

4.80

32

22

50460

42.42

unstable

78.86

-0.375

2.

YP_004928098.1

110

12894.83

4.71

20

12

11920

59.63

unstable

101.18

-0.205

3.

YP_004928060.1

606

65668.79

4.58

66

41

106480

17.53

stable

77.81

-0.271

4.

YP_004928038.1

136

15199.66

6.73

17

17

9970

44.48

unstable

113.38

-0.267

5.

YP_004927994.1

245

27858.82

8.87

35

39

25565

57.76

unstable

94.86

-0.543

6.

YP_004927986.1

206

22816.97

6.12

21

17

40575

68.31

unstable

99.51

-0.127

7.

YP_004927980.1

340

38425.87

5.25

53

39

35870

48.97

unstable

76.12

-0.611

8.

YP_004927975.1

443

49901.31

7.18

56

56

52035

48.98

unstable

78.42

-0.691

9.

YP_004927989.1

242

27935.31

9.93

25

43

36690

45.12

unstable

81.03

-0.683

1

YP_004928003.1

312

33486.89

8.06

23

25

65360

24.16

Stable

76.38

-0.101

1

YP_004928012.1

219

25508.95

6.53

29

28

53650

47.42

unstable

76.58

-0.495

1

YP_004928109.1

289

32660.03

5.70

42

36

39545

51.49

unstable

84.15

-0.410

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