J Cancer 2021; 12(23):7214-7222. doi:10.7150/jca.63517 This issue

Research Paper

Decipher the Helicobacter pylori Protein Targeting in the Nucleus of Host Cell and their Implications in Gallbladder Cancer: An insilico approach

Yunjian Wang1, Ahamad Imran2, Ashwag Shami3 Corresponding address, Anis Ahmad Chaudhary4, Shahanavaj Khan5,6,7 Corresponding address

1. Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou City, Henan Province, 450008, China.
2. King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia.
3. Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia.
4. Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia.
5. Department of Health Sciences, Novel Global Community Educational Foundation, Australia.
6. Department of Bioscience, Shri Ram Group of College (SRGC), Muzaffarnagar, UP, India.
7. Department of Pharmaceutics, College of Pharmacy, PO Box 2457, King Saud University, Riyadh 11451, Saudi Arabia.

This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions.
Citation:
Wang Y, Imran A, Shami A, Chaudhary AA, Khan S. Decipher the Helicobacter pylori Protein Targeting in the Nucleus of Host Cell and their Implications in Gallbladder Cancer: An insilico approach. J Cancer 2021; 12(23):7214-7222. doi:10.7150/jca.63517. Available from https://www.jcancer.org/v12p7214.htm

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Abstract

Graphic abstract

Gallbladder cancer (GBC) is one of the leading causes of cancer-related mortality worldwide. Researchers have investigated that specific strains of bacteria are connected with growth of different types of cancers in human. Some reports show possible implication of Helicobacter pylori (H. pylori) in the etiology of gallbladder cancer (GBC). Their enigmatic mechanisms, nevertheless, are not still well clear. We sought to predict whether various proteins of H. pylori targeted to nucleus of host cells and their implication in growth of gallbladder cancer. GBC is one of the leading causes of cancer mortality worldwide. We applied bioinformatics approach to analyze the H. pylori proteins targeting into the nucleus of host cells using different bioinformatics predictors including nuclear localization signal (NLS) mapper Balanced Subcellular Localization (BaCelLo) and Hum-mPLoc 2.0. Various nuclear targeting proteins may have a potential role in GBC etiology during intracellular infection. We identified 46 H. pylori proteins targeted into nucleus of host cell through bioinformatics tools. These H. pylori nucleus-targeting proteins might alter the normal function of host cells by disturbing the different pathways including replication, transcription, translation etc. Various nucleus-targeted proteins can affect the normal growth and development of infected cells. We propose that H. pylori proteins targeting into the nucleus of host cells regulate GBC growth using different strategies. These integrative bioinformatics research demonstrated several H. pylori proteins that may serve as possible targets or biomarkers for early cure and treatment or diagnosis GBC.

Keywords: Helicobacter pylori, Protein targeting, Host cell, Nucleus, Health informatics, Gallbladder cancer

Introduction

Cancer is the second leading cause of death in the United States and a predominant public health problem worldwide [1]. Gallbladder cancer (GBC) is the fifth most common gastrointestinal cancer worldwide with poor prognosis [2-4]. The number of new cases of GBC and other biliary cancers in the United States was estimated to be approximately 11,740, with 3,830 deaths reported in 2016 [1]. GBC is most frequently associated with the biliary tract. GBC shows the highest incidence in the sixth and seventh decades of life, and females are affected two to six times more often than males [2, 5, 6]. Although GBC is more common in Korea, Japan, Northern India, and Eastern European countries, elevated incidence rates have been observed in Latin America [7]. The infections of different types of bacteria are associated with the progress and development of many diseases including typhoid, diarrhea and different types of cancer [8-10]. Various factors are involved in the process of carcinogenesis for the growth of different types of cancer such as exposure to specific chemicals, obesity, diet, reproductive factors, hepato-biliary anomalies, cholelithiasis (particularly mixed gallstone or gallstone disease), and poor prognosis, unsatisfactory treatment [4], and late diagnosis of chronic gallbladder infections [11]. Similarly different factors have been associated with the growth and progression of GBC. The percentage of patients suffering from GBC after cholecystectomy for assumed gallbladder stone disease is 0.5-1.5% [12]. In addition, genetic disorders such as Peutz-Jegher syndrome, anomalous pancreaticobiliary ductal union, and multiple familial polyposis/Gardener syndrome are associated with GBC [13-15]. The relationship between life style, genetic predisposition, and previous infection in GBC is not well understood [7]. The existence of H. pylori and H. bilis, both in the bile and gallbladder, was confirmed in more than 75% of patients with GBC and more than 50% of patients with chronic cholecystitis that underwent surgery [16-18]. H. pylori is a gram-negative, micro-aerophilic, spiral-shaped, flagellated, and slow-growing bacterium and probably the cause of the most common chronic bacterial infections in humans, present in almost half of the world's population [19, 20]. KHP30 phage observed to be associated as an episome with NY43 strain of H. pylori [21, 22].

Recent reports have indicated the presence of H. pylori in the gallbladders and bile of approximately 75% of patients with GBC and about 50% of patients with chronic cholecystitis [18]. Although studies have revealed some possible mechanisms involved in biliary carcinogenesis, most key events and specific connections to H. pylori infection in this multifaceted cascade that directs the transformation of epithelial cells in the gallbladder remain unknown and require additional investigation. The aim of the present work was to determine H. pylori proteins that are localized into the host cell nucleus and their potential associations with GBC. In this study, we focused on the association between chronic H. pylori infection and GBC development.

Materials and methods

Retrieve the H. pylori proteome

We performed various specified searches to retrieve the whole proteome of H. pylori. Eventually we were focused to the UniProt (Universal Protein Resource) database to predict the nucleus-targeting proteins of H. pylori in the host cell [23]. This UniProt database developed through the collection of PIR protein database, SWISS-PROT, and TrEMBL [23-25] contains immense information regarding the H. pylori proteome. The proteomes of various strains of H. pylori such as strains ATCC 700392/26695 and ATCC 27545, are available in these databases [21, 26].

Selection of a predictive computational tool

The whole proteome of H. pylori strain ATCC 700392/26695 was selected for the prediction of nucleus-targeting proteins in human gallbladder cells. We were used different tools including ExPASy Compute pI/Mw tool, cNLS mapper, Balanced Subcellular Localization (BaCelLo) and Hum-mPLoc 2.0 bioinformatics predictor.

Prediction of pI values and MWs using the ExPASy Compute pI/Mw tool

The ExPASy Compute pI/Mw tool was used to predict the theoretical isoelectric point (pI) and molecular weight (MW) of the query sequence of a particular protein [27]. The tool was utilized to access the extensive annotations available in the SWISS-PROT database [24].

Prediction of NLS in the H. pylori proteome using cNLS mapper

We were used cNLS predictor to analyze the possible monopartite and bipartite NLSs in whole protein sequences of H. pylori proteome [28]. NLS prediction may be used to predict the nucleus-targeting ability of specific proteins [28]. The cNLS predictor shows NLS values in the form of an NLS cut-off, and protein sequences with cut-off values of 10 to 8, 7 to 8, 5 to 3, and 1 to 2 were identified as absolutely targeting the nucleus, partly targeting the nucleus, targeting both the cytoplasm and nucleus, and targeting the cytoplasm, respectively. Moreover, protein sequences with cut-off values between two ranges were rounded to the closest whole integer.

Prediction of protein targeting using the BaCelLo predictor

H. pylori proteins targeting the nucleus of the host cell were predicted using BaCelLo [29]. This predictor may be used to identify proteins in organisms of three different kingdoms (Fungi, Plants, and Animals). In the current study, we analyzed proteins of the organisms from the animal kingdom. The BaCelLo predictor is a computational tool based on diverse support vector machines (SVMs) structured in a decision tree [29].

Selection of BaCeILo-predicted proteins using the Hum-mPLoc 2.0 predictor

H. pylori proteins targeting the nucleus and other compartments in humans were predicted by utilizing the Hum-mPLoc 2.0 subcellular localization predictor [30]. This predictor is based on a top-down approach to increase the power to predict human proteins targeting subcellular components, including the nucleus. Hum-mPLoc 2.0 predicted 14 different classes of subcellular localization, including the nucleus, mitochondrion, cytoplasm, centriole, endoplasmic reticulum, Golgi apparatus, and lysosome, etc.

Results

Search for the H. pylori proteome

UniProt is a comprehensive database that includes the whole H. pylori proteome. We select the ATCC 700392/26695 strain of H. pylori because it had the highest number of proteins (1,552) identified among the available proteomes [26].

Selection of computational tools for the prediction study

In the current study, we employed the ExPASy Compute pI/Mw tool to predict the pI and MW of proteins, cNLS mapper to determine NLSs, BaCelLo to identify proteins targeting different components of host cells, and Hum-mPLoc 2.0 to predict proteins targeting the nucleus of the host cell because of the relative specificities of their predictive approaches (Fig. 1).

Prediction of pI values and MWs using the ExPASy Compute pI/Mw tool

The ExPASy Compute pI/Mw tool calculated theoretical pI values and MWs of proteins in the H. pylori proteome (Fig. 2 and Table 1).

The pI values showed no consistent pattern of proteins targeting in the nucleus of the host cell [31, 32]. However, the maximum number of nucleus-targeting proteins (14 proteins) was observed in the pI range of 8.0-9.0. Increase in the MWs, consistently decreased the frequency of nuclear targeting proteins, except in the 0-20 kDa range (Fig. 2 and Table 1). The least proteins targeting observed in the nucleus of the host cell with MW > 80 kDa (Fig. 2 and Table 1).

 Figure 1 

The image shows the method use for the prediction of nuclear targeting proteins using in silico approach.

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 Figure 2 

In silico analysis of H. pylori proteins that target the nucleus of host cells and their relationship to different parameters.

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 Figure 3 

In silico analysis of total H. pylori proteins in host cells and their relationship to different parameters.

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 Table 1 

In silico analysis of Helicobacter pylori proteins targeted to the host cell nuclei their relation to all proteins with similar molecular weight

S. no.Molecular weight (kW)Number of proteins targeting nucleusTotal number of proteinsPercentage
10-20144343.22
220-40156022.49
340-6093262.76
460-8051054.76
5> 803863.48

Prediction of NLSs in the H. pylori proteome using the cNLS mapper

We utilized the cNLS mapper to analyze NLSs in whole protein sequences of the H. pylori proteome. Both monopartite and bipartite NLSs in the H. pylori proteome were determined (Fig. 3). Proteins with NLS cutoff values of 3.0-5.0 were reported to mostly target the nucleus of the host cell with monopartite NLSs (Table 3). Proteins with NLS cutoff values of 0-3.0 were mostly found to target the nucleus of the host cell with bipartite NLSs (Table 3).

Prediction of protein targeting using the BaCelLo predictor

A total of 85 (out of 1,552) proteins in the H. pylori proteome were predicted to target the nucleus of the host cell using the BaCeILo predictor [29]. The details of H. pylori proteins that target the host cell nucleus based on various parameters are shown in Table 4.

Selection of BaCeILo-predicted proteins using the Hum-mPLoc 2.0 predictor

Only 46 proteins were consistently shown to target the nucleus of the host cell by the software of Hum-mPlooc 2.0 [30]. Fig. 2 and Fig. 3 illustrate the patterns of H. pylori proteins targeting host cell nucleus according to different parameters. Moreover, the details of the 46 proteins along with their functions are shown in Table 4.

Discussion

Various studies have revealed the different possible factors involved in the development of cancer, including genetic factors, gender, age, diet, consumption of tobacco, inflammation, and infections by various pathogens. Infection is considered a leading factor involved in the development of about 16% of cancers [33]. It has confirmed that various specific bacterial strains have the ability to alter numerous pathways and molecular events in the host cell for their own survival and involved in the growth and development of different types of cancer [10, 32, 34]. In a report Arthur et. al (2012) demonstrated the involvement of E. coli NC101 strain in the progression of invasive carcinoma in azoxymethane (AOM)-treated Il10(-/-) mice. We have illustrated the involvement of mycoplasma hominis and Chlamydia pneumoniae protein targeting and their implication in the progression of prostate cancer and lungs cancer in recently published study [31, 32, 34]. It was only in the early 1990s that the role of H. pylori as a causative agent of cancer was highlighted [35]. The molecular mechanisms underlying gallbladder carcinogenesis remain unclear even today. We have proposed that various nucleus-targeting proteins of H. pylori alter the normal function of host cells. pI values failed to explain the pattern for nuclear targeting (Table 2). The association between H. pylori proteins that targeted the host cell nucleus and various parameters is shown in Fig. 2. The process of targeting the host nucleus is a key event that involves the regulation of the host cell. This is generally analyzed through specific motifs in protein sequences called NLSs. The NLS predictor allows prediction of the possible activity of an NLS in the amino acid sequences of different proteins. Various predictors may analyze the specific motifs in the amino acid sequences. The NLS mapper identified six classes of NLSs such that the nuclear import proteins are transported through the α/β pathways of importin. Therefore, we utilized the NLS mapper in our study to predict NLS activity in both monopartite and bipartite NLSs (enriched basic amino acid stretches) [36]. The NLS predictor identified potential localization sites of the proteins, including the nucleus, partially in the nucleus, the cytoplasm, and equally in both the cytoplasm and nucleus of the host cell.

 Table 2 

In silico analysis of H. pylori proteins targeted to the host cell nucleus and their relation to all proteins with similar pI value

S. no.Isoelectric pointNumber of proteins targeting nucleiTotal number of proteinsPercentage
13.0-5.05647.81
25.0-6.062732.19
36.0-7.052452.04
47.0-8.061274.72
58.0-9.0143304.24
69.0-10.0104502.22
710.0-11.00520
811.0-13.00120
 Table 3 

In silico analysis of H. pylori proteins targeted to the host cell nucleus and their relation to all proteins with similar monopartite and bipartite nuclear localization signals (NLS)

NLSNLS cut-offNumber of proteins targeting nucleusTotal number of proteinsPercentage
Monopartite0-3.0513770.36
Monopartite3.0-5.02210121.78
Monopartite5.0-8.0196230.64
Monopartite> 8.00130
Bipartite0-3.04227115.49
Bipartite3.0-5.028270.24
Bipartite5.0-8.014410.22
Bipartite> 8.01147.14
 Table 4 

Descriptions of Helicobacter pylori proteins targeted into the nucleus of host cells as predicted using various tools

Accession numberProtein nameFunction in bacteriaEvidence of proteinIsoelectric pointMolecular weight in daltonsNLS Mapper
Monopartite Bipartite
BaCeILoHum-mPLoc 2.0
P55973Translation initiation factor IF-3Translation initiation factor activityProtein inferred from homology9.572334204.9NucleusNucleus
P56131tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase (EC 2.8.4.3) (Dimethylallyl)adenosine tRNA methylthiotransferase MiaB) (tRNA-i(6)A37 methylthiotransferase)4 iron, 4 sulfur cluster binding, metal ion binding, transferase activityProtein inferred from homology8.754942305.5NucleusNucleus
O25029DEAD-box ATP-dependent RNA helicase RhpA (EC 3.6.4.13)ATP binding, helicase activity, RNA bindingExperimental evidence at the protein level8.785580626.3NucleusNucleus
P56398Ribosome-recycling factor (RRF) (Ribosome-releasing factor)TranslationProtein inferred from homology7.792091503.7NucleusNucleus
O26061Flavin-dependent thymidylate synthase (FDTS) (EC 2.1.1.148) (FAD-dependent thymidylate synthase) (Thymidylate synthase ThyX) (TS) (TSase)Flavin adenine dinucleotide binding, thymidylate synthase (FAD) activityExperimental evidence at the protein level6.762407103.2NucleusNucleus
P55991DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I) (Omega-protein) (Relaxing enzyme) (Swivelase) (Untwisting enzyme)DNA binding, DNA topoisomerase type I activity, metal ion bindingExperimental evidence at the protein level9.048319624.9NucleusNucleus
P55986Uncharacterized RNA pseudouridine synthase HP_1459 (EC 5.4.99.-) (RNA pseudouridylate synthase) (RNA-uridine isomerase)Pseudouridine synthase activity, RNA bindingProtein inferred from homology9.93022836.8NucleusNucleus
O25506DNA-binding protein HUDNA bindingProtein inferred from homology9.051038405.8NucleusNucleus
O25242DNA polymerase III subunit beta (EC 2.7.7.7)3'-5' exonuclease activity, DNA binding, DNA-directed DNA polymerase activityExperimental evidence at the protein level5.514218504.2NucleusNucleus
P57798Putative Fe (2+) transport protein AIon transport, iron, ion homeostasisProtein inferred from homology8.62871905.8NucleusNucleus
O25929Flagellar assembly factor FliW 2Bacterial-type flagellum assembly, regulation of translationExperimental evidence at the protein level5.921486202.8NucleusNucleus
P55976Transcription termination/antitermination protein NusGDNA-templated transcription, termination, regulation of DNA-templated transcription, elongation, transcription antiterminationProtein inferred from homology6.982026102.9NucleusNucleus
P55993RNA polymerase sigma factor RpoD (Sigma-70)DNA binding, DNA binding transcription factor activity, sigma factor activityExperimental evidence at the protein level7.947773745.2NucleusNucleus
P56123Ribonuclease R (RNase R) (EC 3.1.13.1) (VacB protein homolog)Exoribonuclease II activity, RNA bindingProtein inferred from homology9.177416304.4NucleusNucleus
P6662130S ribosomal protein S8rRNA binding, structural constituent of ribosomeProtein inferred from homology9.781518404.3NucleusNucleus
O25475Protein translocase subunit SecAATP binding, metal ion bindingProtein inferred from homology5.629908405.6NucleusNucleus
Q09064Urease accessory protein UreENickel cation bindingExperimental evidence at the protein level8.581938205.4NucleusNucleus
O25448Flagellar protein FliSBacterial-type flagellum assemblyExperimental evidence at the protein level5.031454300NucleusNucleus
O25684Response regulatorDNA bindingExperimental evidence at the protein level5.222546803.1NucleusNucleus
O25998Secreted protein involved in flagellar motilityUnknownExperimental evidence at the protein level6.542048033.3NucleusNucleus
O25262Cag pathogenicity island protein (Cag7)UnknownProtein predicted5.612194012.56.8NucleusNucleus
O25085Uncharacterized proteinUnknownProtein predicted6.741530405.4NucleusNucleus
O24903Uncharacterized proteinUnknownProtein predicted5.245740887.5NucleusNucleus
O25555Uncharacterized proteinUnknownProtein predicted8.81471405NucleusNucleus
O25800Uncharacterized proteinUnknownProtein predicted9.453063204.4NucleusNucleus
O25576Uncharacterized proteinMetal ion bindingProtein predicted10.131613703.3NucleusNucleus
O25834Uncharacterized proteinUnknownProtein predicted5.572214955.7NucleusNucleus
O24939Uncharacterized proteinUnknownProtein predicted9.544526424.3NucleusNucleus
O24937Uncharacterized proteinUnknownProtein predicted9.464513603.9NucleusNucleus
O25553Uncharacterized proteinUnknownProtein predicted9.791135606.6NucleusNucleus
O25652Conjugal transfer protein (TraG)Unidirectional conjugationProtein predicted8.892044204NucleusNucleus
O25650Uncharacterized proteinUnknownProtein predicted8.763260006.5NucleusNucleus
O25105Uncharacterized proteinUnknownProtein predicted9.812197804.5NucleusNucleus
O25188DNA topoisomerase (EC 5.99.1.2)DNA binding, DNA topoisomerase type I activityProtein inferred from homology8.477767705.8NucleusNucleus
O25799Uncharacterized proteinUnknownProtein predicted9.564399403.5NucleusNucleus
O25195Uncharacterized proteinUnknownProtein predicted5.364143705.1NucleusNucleus
O24905Uncharacterized proteinUnknownProtein predicted4.731408602.7NucleusNucleus
O25102Uncharacterized proteinUnknownProtein predicted6.56698902.1NucleusNucleus
O25304Uncharacterized proteinTransportProtein predicted9.463738204.3NucleusNucleus
O25419DNA polymerase III gamma and tau subunits (DnaX)ATP binding, DNA-directed DNA polymerase activityProtein predicted5.876624504.8NucleusNucleus
O25379Uncharacterized proteinATP binding, DNA binding, hydrolase activityProtein predicted8.056876010.56.4NucleusNucleus
O25131Uncharacterized proteinUnknownProtein predicted7.852321106.1NucleusNucleus
O25010Uncharacterized proteinRegulation of transcription, DNA-templatedProtein predicted9.52859904.2NucleusNucleus
O25373Uncharacterized proteinUnknownProtein predicted8.934763304.7NucleusNucleus
O25265Cag pathogenicity island protein (Cag10)UnknownProtein predicted9.542909505.9NucleusNucleus
O34550IS200 insertion sequence from SARA17DNA binding, transposase activityProtein predicted8.441596504.6NucleusNucleus

In addition, BaCeILo and Hum-mPLoc 2.0 were employed in the current study to analyze H. pylori protein targeting to different host cell compartments. The results of BaCeILo and Hum-mPLoc 2.0 revealed the variation in protein targeting to the nucleus because of the utilization of different datasets during prediction. Such differences in the results from various predictors are acceptable. The Hum-mPLoc predictor analyzes the targeting of proteins to different compartments of cells using sequential evolution and domain information. The predictor computes 14 subcellular compartments such as the nucleus, mitochondrion, cytoplasm, endoplasmic reticulum, lysosome, Golgi apparatus, plasma membrane, and peroxisome. Proteins with MW < 40 kDa may be transported to the nucleus through passive transport mechanisms [28]. In the present study, we predicted various H. pylori proteins with MW < 40 kDa that affected the normal pathways of cells and may be involved in the progression of GBC. Furthermore, the nucleus-targeting proteins in humans determined by Hum-mPLoc 2.0 were compared with those determined by BaCelLo to more accurately define the subcellular localization of H. pylori proteins. The Hum-mPLoc 2.0 predictor confirmed only 46 H. pylori proteins that were targeted to the nuclei of host cells.

We focused on evaluating the involvement of the nucleus-targeting proteins of H. pylori in the progression and development of GBC. H. pylori-derived effector proteins may alter the host cell internal environment through the induction of immunosuppression, suppression of tumor suppressor genes, activation of chronic inflammation, and transformation of normal cells [37].

H. pylori proteins that target the nuclei of host cells and their implications in GBC

From the whole H. pylori proteome with 1,552 proteins, only 46 proteins were predicted to be targeted to the host cell nucleus during intracellular infection. This specific targeting may alter the homeostasis of normal cells. The results of the current study should be validated through experimental research in wet laboratories prior to drawing any final conclusions. The corresponding results may be used to develop therapies to manage and cure cancer.

Replication, DNA binding, and DNA repair in the development of GBC

Various factors such as genomic instability determine cancer susceptibility. However, the molecular mechanisms that lead to the development of cancer are incompletely understood. A report showed that H. pylori infection suppressed the expression of p53 protein [38]. A prominent hypothesis is that alterations in replication or the establishment of error-prone DNA synthesis phenotypes originating in genomic instability may serve as a source of cancer [39]. Progression of cancer is affected by different DNA-binding proteins such as the methyl CpG-binding protein, which detects the methylation of DNA and its components. Together these proteins play an important role in the development of cancer [40]. Furthermore, the tightly controlled DNA replication is essential for the multiplication of normal cells, and mutations in proteins involved in DNA replication have been associated with the development of different types of cancers [41, 42].

Diverse DNA-binding proteins have been predicted to target the nuclei of host cells, including DNA topoisomerase 1 (accession no. P55991), DNA polymerase III subunit beta (accession no. O25242), ribonuclease R (RNase R) (accession no. P56123), DNA topoisomerase (accession no. O25188), DNA polymerase III gamma and tau subunits (accession no. O25419), and the IS200 insertion sequence from SARA17 (accession no. O34550). These nucleus-targeting proteins and other uncharacterized proteins may affect the replication process in the nucleus of the host cell. The functions and other details of these proteins are shown in Table 4. Bacterial insertion sequences IS200 and IS607 encode a transposase (TnpA) and one protein with unknown function (TnpB) that is believed to act as a methyltransferase [43]. The levels of methyltransferase are increased in some cancer cell lines and cancer tissues, wherein these enzymes may be involved in the hypermethylation of the promoter CpG-rich regions of the tumor suppressor genes [44].

Transcription and translation regulatory proteins in the development of GBC

The progression from normal to cancerous cells is associated with alterations in protein-protein interactions, either in the transcription or translation regulatory proteins. The dysregulation in the expression of various genes may lead to the suppression of different anti-oncogenes and activation of proto-oncogenes during bacterial infection [45]. Conserved structural similarities in different subunits of RNA polymerase as well as antigenicity are specific features of eukaryotes. The current study showed that H. pylori RNA polymerase sigma factor RpoD (accession no. P55993), response regulator (accession no. O25684), and transcription termination/antitermination protein NusG (accession no. P55976) target the host cell nucleus and may alter the normal pathways in the host cell. The unfolded response regulator has been reported as a new predictive biomarker for the identification of cancers [46]. Nevertheless, the possible involvement of such proteins in the dysregulation of normal pathways must be experimentally demonstrated before making final conclusions.

Various H. pylori translation regulatory proteins similarly target the host cell nucleus, including translation initiation factor IF-3 (accession no. P55973), ribosome-recycling factor (RRF) (accession no. P56398), and 30S ribosomal protein S8 (accession no. P66621). These proteins also disturb the normal functioning of protein synthesis by altering gene expression. Alterations in gene expression may lead to the progression of GBC.

Uncharacterized proteins in the development of GBC

Various uncharacterized H. pylori proteins were predicted to target the nucleus of the host cell, including Cag pathogenicity island protein (Cag7) (accession no. O25262), Cag pathogenicity island protein (Cag10) (accession no. O25265), and another uncharacterized protein (accession no. O25010). These proteins may also act as factors that promote carcinogenesis in the gallbladder. For instance, CagA may interact with a tumor suppressor protein (RUNX3) that is commonly inactivated in gastric carcinomas [47].

Conclusions

The current work examines the mechanisms underlying the progression of GBC during H. pylori infection and the possible implications of the nucleus-targeting proteins in the development of GBC. The novel findings of this study may suggest new approaches to manage and cure GBC.

Abbreviations

H. pylori: Helicobacter pylori; GBC: Gallbladder cancer; NLS: Nuclear localization signal; BaCelLo: Balanced Subcellular Localization; Hum-mPLoc 2.0.: Human protein subcellular localization; UniProt: Universal Protein Resource; pI: Isoelectric point; MW: Molecular weight.

Acknowledgements

This research was funded by the Deanship of Scientific Research at Princess Nourah bint Abdulrahman University through the Fast-track Research Funding Program.

Availability of data and materials

Data of whole proteome of H. pylori with Proteome ID UP000000429 have download from UniProt database (https://www.uniprot.org/uniprot/?query=taxonomy:85962) in current study.

Competing Interests

The authors have declared that no competing interest exists.

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Author contact

Corresponding address Corresponding authors: Dr. Shahanavaj Khan, E-mail: sdkhanedu.sa; Tel.: +91-921-999-3262; Department of Biosciences, Shri Ram Group of College (SRGC), Muzaffarnagar 251001, India; Department of Pharmaceutics, College of Pharmacy, P.O. Box 2457, King Saud University, Riyadh 11451, Saudi Arabia; Novel Global Community Educational Foundation, Australia. Dr, Ashwag Shami, E-mail: ayshamiedu.sa; Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia.


Received 2021-6-4
Accepted 2021-10-3
Published 2021-10-25