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Global genomic and proteomic analysis indicates co-evolution of Neisseria species and with their human host

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Abstract

Neisseria, a genus from the beta-proteobacteria class, is of potential clinical importance. This genus contains both pathogenic and commensal strains. Gonorrhea and meningitis are two major diseases caused by pathogens belonging to this genus. With the increased use of antimicrobial agents against these pathogens they have evolved the antimicrobial resistance capacity making these diseases nearly untreatable. The set of anti-bacterial resistance genes (resistome) and genes associated with signal processing (secretomes) are crucial for the host-microbial interaction. With the virtue of whole-genome sequences and computational biology, it is now possible to study the genomic and proteomic riddles of Neisseria along with their comprehensive evolutionary and metabolic profiling. We have studied relative synonymous codon usage, amino acid usage, reverse ecology, comparative genomics, evolutionary analysis and pathogen-host (Neisseria-human) interaction through bioinformatics analysis. Our analysis revealed the co-evolution of Neisseria genomes with the human host. Moreover, the co-occurrence of Neisseria and humans has been supported through reverse ecology analysis. A differential pattern of the evolutionary rate of resistomes and secretomes was evident among the pathogenic and commensal strains. Comparative genomics supported the presence of virulent genes in both pathogenic and commensal strains of the select genus. Our analysis also indicated a transition from commensal to pathogenic Neisseria strains through the long run of evolution.

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Abbreviations

AMR :

Anti-microbial resistance

STD :

Sexually transmitted disease

MLA :

Multi-locus alignment

NJ :

Neighbor-joining

KO :

KEGG ontology

CUB :

Codon usage bias

GC :

Total guanine and cytosine

GC3 :

Total guanine and cytosine at third position of codons

Fop :

Frequency of optimal codons

tAI :

TRNA adaptation index

Enc :

Effective number of codons

CAI :

Codon adaptation index

PEC :

Protein energy cost

RSCU :

Relative synonymous codon usage

PHX genes :

Potentially highly expressed genes

PLX genes :

Potentially lowly expressed genes

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Authors and Affiliations

  1. Salim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641 108, India

    Indrani Sarkar & Prateek Dey

  2. Mahatma Gandhi Central University, Motihari, Bihar, 845401, India

    Saurabh Singh Rathore

  3. Bihar Veterinary College, Patna, Bihar, 800014, India

    Gyan Dev Singh

  4. Department of Life Science, Central University of South Bihar, Gaya, Bihar, 824236, India

    Ram Pratap Singh

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  1. Indrani Sarkar
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  2. Prateek Dey
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  4. Gyan Dev Singh
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Contributions

RPS, IS, GDV and SSR conceived the idea. IS and PD curated the data and performed all analyses. RPS, IS, PD, SSR, GDV wrote the manuscript. All authors have agreed to the final version of the manuscript.

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Correspondence to Ram Pratap Singh.

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Supplementary Information

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11274_2022_3338_MOESM1_ESM.xlsx

Supplementary file1 (XLSX 227 kb)— KEGG ID of metabolic compounds shared between the selected 21 Neisseria species and human host are given under the heading ‘Edge list’. ‘Seed set’ are those which are to be taken exogenously and confidence level is the probability of a seed. Based upon this interaction, competition and complementation index were calculated and a metabolic network was generated.

11274_2022_3338_MOESM2_ESM.xlsx

Supplementary file2 (XLSX 11 kb)—List of human proteins associated with Gonorrhoea as obtained from DisGenet server. DSI_g of more than 0.7 was used as a cut-off.

11274_2022_3338_MOESM3_ESM.xlsx

Supplementary file3 (XLSX 9 kb)— List of human proteins associated with Meningitis as obtained from DisGenet server. DSI_g of more than 0.7 was used as a cut-off.

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Sarkar, I., Dey, P., Rathore, S.S. et al. Global genomic and proteomic analysis indicates co-evolution of Neisseria species and with their human host. World J Microbiol Biotechnol 38, 149 (2022). https://doi.org/10.1007/s11274-022-03338-w

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