Comparative genomic analysis of novel Acinetobacter symbionts

A combined systems biology and genomics approach

Vipin Gupta, Shazia Haider, Utkarsh Sood, Jack A. Gilbert, Meenakshi Ramjee, Ken Forbes, Yogendra Singh, Bruno S. Lopes, Rup Lal

Research output: Contribution to journalArticle

4 Citations (Scopus)
6 Downloads (Pure)

Abstract

The increasing trend of antibiotic resistance in Acinetobacter drastically limits the range of therapeutic agents required to treat multidrug resistant (MDR) infections. This study focused on analysis of novel Acinetobacter strains using a genomics and systems biology approach. Here we used a network theory method for pathogenic and non-pathogenic Acinetobacter spp. to identify the key regulatory proteins (hubs) in each strain. We identified nine key regulatory proteins, guaA, guaB, rpsB, rpsI, rpsL, rpsE, rpsC, rplM and trmD, which have functional roles as hubs in a hierarchical scale-free fractal protein-protein interaction network. Two key hubs (guaA and guaB) were important for insect-associated strains, and comparative analysis identified guaA as more important than guaB due to its role in effective module regulation. rpsI played a significant role in all the novel strains, while rplM was unique to sheep-associated strains. rpsM, rpsB and rpsI were involved in the regulation of overall network topology across all Acinetobacter strains analyzed in this study. Future analysis will investigate whether these hubs are useful as drug targets for treating Acinetobacter infections.

Original languageEnglish
Article number29043
Pages (from-to)1-12
Number of pages12
JournalScientific Reports
Volume6
DOIs
Publication statusPublished - 5 Jul 2016

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Acinetobacter
Systems Biology
Genomics
Acinetobacter Infections
Protein Interaction Maps
Fractals
Proteins
Microbial Drug Resistance
Insects
Sheep
Infection
Pharmaceutical Preparations
Therapeutics

Cite this

Gupta, V., Haider, S., Sood, U., Gilbert, J. A., Ramjee, M., Forbes, K., ... Lal, R. (2016). Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach. Scientific Reports, 6, 1-12. [29043]. https://doi.org/10.1038/srep29043

Comparative genomic analysis of novel Acinetobacter symbionts : A combined systems biology and genomics approach. / Gupta, Vipin; Haider, Shazia; Sood, Utkarsh; Gilbert, Jack A.; Ramjee, Meenakshi; Forbes, Ken; Singh, Yogendra; Lopes, Bruno S.; Lal, Rup.

In: Scientific Reports, Vol. 6, 29043, 05.07.2016, p. 1-12.

Research output: Contribution to journalArticle

Gupta, V, Haider, S, Sood, U, Gilbert, JA, Ramjee, M, Forbes, K, Singh, Y, Lopes, BS & Lal, R 2016, 'Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach', Scientific Reports, vol. 6, 29043, pp. 1-12. https://doi.org/10.1038/srep29043
Gupta, Vipin ; Haider, Shazia ; Sood, Utkarsh ; Gilbert, Jack A. ; Ramjee, Meenakshi ; Forbes, Ken ; Singh, Yogendra ; Lopes, Bruno S. ; Lal, Rup. / Comparative genomic analysis of novel Acinetobacter symbionts : A combined systems biology and genomics approach. In: Scientific Reports. 2016 ; Vol. 6. pp. 1-12.
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abstract = "The increasing trend of antibiotic resistance in Acinetobacter drastically limits the range of therapeutic agents required to treat multidrug resistant (MDR) infections. This study focused on analysis of novel Acinetobacter strains using a genomics and systems biology approach. Here we used a network theory method for pathogenic and non-pathogenic Acinetobacter spp. to identify the key regulatory proteins (hubs) in each strain. We identified nine key regulatory proteins, guaA, guaB, rpsB, rpsI, rpsL, rpsE, rpsC, rplM and trmD, which have functional roles as hubs in a hierarchical scale-free fractal protein-protein interaction network. Two key hubs (guaA and guaB) were important for insect-associated strains, and comparative analysis identified guaA as more important than guaB due to its role in effective module regulation. rpsI played a significant role in all the novel strains, while rplM was unique to sheep-associated strains. rpsM, rpsB and rpsI were involved in the regulation of overall network topology across all Acinetobacter strains analyzed in this study. Future analysis will investigate whether these hubs are useful as drug targets for treating Acinetobacter infections.",
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