Molecular Evolution of Extremophiles

Chakravorty, Debamitra; Shreshtha, Ashwinee Kumar; Babu, Vijay; Patra, Sanjukta

doi:10.1002/9781118394144.ch1

Cited by 4 publications

(3 citation statements)

References 101 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genomic and proteomic level adaptations are two amongst them. Each level comprises of numerous attributes which requires further exploration 5 , 6 . It has been done usually through comparing their genomic features, sequence and order of genes, codon usage pattern, gene regulation and expression.…”

Section: Introductionmentioning

confidence: 99%

Deciphering the rationale behind specific codon usage pattern in extremophiles

Khan

Patra

2018

Sci Rep

Self Cite

View full text Add to dashboard Cite

Protein stability is affected at different hierarchies – gene, RNA, amino acid sequence and structure. Gene is the first level which contributes via varying codon compositions. Codon selectivity of an organism differs with normal and extremophilic milieu. The present work attempts at detailing the codon usage pattern of six extremophilic classes and their harmony. Homologous gene datasets of thermophile-mesophile, psychrophile-mesophile, thermophile-psychrophile, acidophile-alkaliphile, halophile-nonhalophile and barophile-nonbarophile were analysed for filtering statistically significant attributes. Relative abundance analysis, 1–9 scale ranking, nucleotide compositions, attribute weighting and machine learning algorithms were employed to arrive at findings. AGG in thermophiles and barophiles, CAA in mesophiles and psychrophiles, TGG in acidophiles, GAG in alkaliphiles and GAC in halophiles had highest preference. Preference of GC-rich and G/C-ending codons were observed in halophiles and barophiles whereas, a decreasing trend was reflected in psychrophiles and alkaliphiles. GC-rich codons were found to decrease and G/C-ending codons increased in thermophiles whereas, acidophiles showed equal contents of GC-rich and G/C-ending codons. Codon usage patterns exhibited harmony among different extremophiles and has been detailed. However, the codon attribute preferences and their selectivity of extremophiles varied in comparison to non-extremophiles. The finding can be instrumental in codon optimization application for heterologous expression of extremophilic proteins.

show abstract

Section: Introductionmentioning

confidence: 99%

Deciphering the rationale behind specific codon usage pattern in extremophiles

Khan

Patra

2018

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…In the last 30 years, the fascinating world of microorganisms able not only to survive but also to proliferate at extreme conditions has attracted researchers in several multidisciplinary scientific fields. Spanning through the three domains of life, such microorganisms, known as extremophiles, were roughly distinguished on the basis of their optimal growth conditions [ 1 , 2 ]. Within this frame, halophiles are organisms that require highly saline conditions for survival and proliferation.…”

Section: Introductionmentioning

confidence: 99%

“…Within this frame, halophiles are organisms that require highly saline conditions for survival and proliferation. They inhabit various types of NaCl-saturated environments occurring throughout Earth’s biosphere, spanning a wide range of scales from solar salterns, inland salt-lakes, and deep-sea hypersaline anoxic brines (DHABs) [ 1 , 2 ].…”

Section: Introductionmentioning

confidence: 99%

The Deep-Sea Polyextremophile Halobacteroides lacunaris TB21 Rough-Type LPS: Structure and Inhibitory Activity towards Toxic LPS

et al. 2017

View full text Add to dashboard Cite

The structural characterization of the lipopolysaccharide (LPS) from extremophiles has important implications in several biomedical and therapeutic applications. The polyextremophile Gram-negative bacterium Halobacteroides lacunaris TB21, isolated from one of the most extreme habitats on our planet, the deep-sea hypersaline anoxic basin Thetis, represents a fascinating microorganism to investigate in terms of its LPS component. Here we report the elucidation of the full structure of the R-type LPS isolated from H. lacunaris TB21 that was attained through a multi-technique approach comprising chemical analyses, NMR spectroscopy, and Matrix-Assisted Laser Desorption Ionization (MALDI) mass spectrometry. Furthermore, cellular immunology studies were executed on the pure R-LPS revealing a very interesting effect on human innate immunity as an inhibitor of the toxic Escherichia coli LPS.

show abstract

Insertion sequences enrichment in extreme Red sea brine pool vent

2016

View full text Add to dashboard Cite

Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world's largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep. We report a gradient in the abundance of mobile genetic elements, dramatically increasing in the harshest environment of the pool. Additionally, we identified a strong association between the abundance of insertion sequences and extreme conditions, being highest in the harshest and deepest layer of the Red Sea Atlantis II Deep. Our comparative analyses of mobile genetic elements in secluded, extreme and relatively non-extreme environments, suggest that insertion sequences predominantly contribute to polyextremophiles genome plasticity.

show abstract

Molecular Evolution of Extremophiles

Cited by 4 publications

References 101 publications

Deciphering the rationale behind specific codon usage pattern in extremophiles

Deciphering the rationale behind specific codon usage pattern in extremophiles

The Deep-Sea Polyextremophile Halobacteroides lacunaris TB21 Rough-Type LPS: Structure and Inhibitory Activity towards Toxic LPS

Insertion sequences enrichment in extreme Red sea brine pool vent

Contact Info

Product

Resources

About