Crystallographic and modelling studies on Mycobacterium tuberculosis RuvA

Prabu, J.R.; Thamotharan, Subbiah; Khanduja, Jasbeer Singh; Chandra, Nagasuma; Muniyappa, K.; Vijayan, M.

doi:10.1016/j.bbapap.2009.04.003

Cited by 24 publications

(9 citation statements)

References 58 publications

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“…Therefore, the actual consequences of these five amino acid changes on RuvA functionality cannot be directly tested. Nevertheless, to hint at the potential functional consequences of these amino acid changes, we reviewed the literature and collated a list of 51 amino acid sites in the approximately 200 amino acid-long RuvA protein that are considered important for proper folding, multimerization or DNA binding, based on crystallography (Rafferty et al 1996; Nishino et al 1998, 2000; Roe et al 1998; Ariyoshi et al 2000; Yamada et al 2002; Prabu et al 2006, 2009) or mutagenesis studies (Nishino et al 1998; Privezentzev et al 2005; Baharoglu et al 2008; Fujiwara et al 2008; Le Masson et al 2008; Mayanagi et al 2008; Bradley et al 2011). We found that one amino acid change inducing a physicochemical modification in isopod Wolbachia RuvA falls in this list of 51 important amino acids (Lys-118).…”

Section: Resultsmentioning

confidence: 99%

Signs of Neutralization in a Redundant Gene Involved in Homologous Recombination in Wolbachia Endosymbionts

Badawi¹,

Giraud²,

Vavre³

et al. 2014

Genome Biology and Evolution

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Genomic reduction in bacterial endosymbionts occurs through large genomic deletions and long-term accumulation of mutations. The latter process involves successive steps including gene neutralization, pseudogenization, and gradual erosion until complete loss. Although many examples of pseudogenes at various levels of degradation have been reported, neutralization cases are scarce because of the transient nature of the process. Gene neutralization may occur due to relaxation of selection in nonessential genes, for example, those involved in redundant functions. Here, we report an example of gene neutralization in the homologous recombination (HR) pathway of Wolbachia, a bacterial endosymbiont of arthropods and nematodes. The HR pathway is often depleted in endosymbiont genomes, but it is apparently intact in some Wolbachia strains. Analysis of 12 major HR genes showed that they have been globally under strong purifying selection during the evolution of Wolbachia strains hosted by arthropods, supporting the evolutionary importance of the HR pathway for these Wolbachia genomes. However, we detected signs of recent neutralization of the ruvA gene in a subset of Wolbachia strains, which might be related to an ancestral, clade-specific amino acid change that impaired DNA-binding activity. Strikingly, RuvA is part of the RuvAB complex involved in branch migration, whose function overlaps with the RecG helicase. Although ruvA is experiencing neutralization, recG is under strong purifying selection. Thus, our high phylogenetic resolution suggests that we identified a rare example of targeted neutralization of a gene involved in a redundant function in an endosymbiont genome.

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Section: Resultsmentioning

confidence: 99%

Signs of Neutralization in a Redundant Gene Involved in Homologous Recombination in Wolbachia Endosymbionts

Badawi¹,

Giraud²,

Vavre³

et al. 2014

Genome Biology and Evolution

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“…In addition to that on plant lectins, a long range programme of mycobacterial proteins, with special emphasis on TB proteins, is currently under way in this laboratory [68][69][70][71][72][73][74]. Taking a common thread from these two programmes, we have recently initiated work on mycobacterial lectins as well.…”

Section: Mycobacterial Lectins a New Initiativementioning

confidence: 97%

Structural diversity and ligand specificity of lectins. The Bangalore effort

Abhinav

Vijayan

2014

Pure and Applied Chemistry

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Structural studies in this laboratory encompass four of the five major classes of plant lectins, including the one discovered by us. In addition to addressing issues specific to individual lectins, the work provided insights into protein folding, quaternary association and generation of ligand specificity. Legume and β-prism fold lectins constitute families of proteins in which small alterations in essentially the same tertiary structure lead to large variations in quaternary structure, including that involving an open structure. Strategies for generating ligand specificity include water bridges, variation in loop length, post translational modification and oligomerization. Three of the structural classes investigated have subunits with three-fold symmetry. The symmetry in the structure is reflected in the sequence to different extents in different subclasses. The evolutionary implications of this observation have been explored. The work on lectins has now been extended to those from mycobacteria.

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“…We have been following a long-range programme on the structure and interactions of plant lectins (Banerjee et al, 1994;Sankaranarayanan et al, 1996;Vijayan & Chandra, 1999;Ramachandraiah et al, 2003;Jeyaprakash et al, 2004;Singh et al, 2005;Natchiar et al, 2007;Kulkarni et al, 2007;Sharma et al, 2009). The present communication represents the first attempt to extend this work to mycobacterial lectins as part of another ongoing progamme on the structural biology of mycobacterial proteins (Vijayan, 2005;Krishna et al, 2007;Selvaraj et al, 2007;Roy et al, 2008;Kaushal et al, 2008;Prabu et al, 2009;Chetnani et al, 2010).…”

Section: Introductionmentioning

confidence: 93%

Cloning, expression, purification, crystallization and preliminary X-ray studies of a secreted lectin (Rv1419) fromMycobacterium tuberculosis

et al. 2010

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A secreted lectin, Rv1419, from Mycobacterium tuberculosis has been cloned, expressed, purified and crystallized and the crystals have been characterized. This represents the first X-ray investigation of a lectin or lectin-like molecule from the pathogen. The cubic crystals contain one molecule in the asymmetric unit. Sequence comparisons indicate that the lectin has a -trefoil fold and belongs to a well characterized family of carbohydrate-binding modules. Structural analysis of the crystals is in progress.

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Crystallographic and modelling studies on Mycobacterium tuberculosis RuvA

Cited by 24 publications

References 58 publications

Signs of Neutralization in a Redundant Gene Involved in Homologous Recombination in Wolbachia Endosymbionts

Signs of Neutralization in a Redundant Gene Involved in Homologous Recombination in Wolbachia Endosymbionts

Structural diversity and ligand specificity of lectins. The Bangalore effort

Cloning, expression, purification, crystallization and preliminary X-ray studies of a secreted lectin (Rv1419) fromMycobacterium tuberculosis

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