Pathophysiological Implications of Cell Envelope Structure in Mycobacterium tuberculosis and Related Taxa

Minnikin, David E.; Lee, Oona Y-C.; Wu, Houdini H.T.; Nataraj, Vijayashankar; Donoghue, Helen D.; Ridell, Malin; Watanabe, Motoko; LukeAlderwick,; Bhatt, Apoorva; Besra, Gurdyal S.

doi:10.5772/59585

Cited by 30 publications

(34 citation statements)

References 108 publications

(192 reference statements)

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“…However, fundamental details such as how MAs are arranged in the cell wall, and how they interact with immune components, are yet to be determined. Cryo-electron microscopy results suggest that the outer bilayer of the mycobacterial cell wall is 7-8 nm wide and consists of a symmetrical bilayer structure [37][38][39][40]. This observation implies that longer MAs need to fold to fit into this space.…”

Section: Introductionmentioning

confidence: 99%

Revealing solvent-dependent folding behavior of mycolic acids from Mycobacterium tuberculosis by advanced simulation analysis

et al. 2019

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Mycobacterium tuberculosis remains a persistent pathogen, partly due to its lipid rich cell wall, of which mycolic acids (MAs) are a major component. The fluidity and conformational flexibilities of different MAs in the bacterial cell wall significantly influence its properties, function, and observed pathogenicity; thus, a proper conformational description of different MAs in different environments (e.g., in vacuum, in solution, in monolayers) can inform about their potential role in the complex setup of the bacterial cell wall. Previously, we have shown that molecular dynamics (MD) simulations of MA folding in vacuo can be used to characterize MA conformers in seven groupings relating to bending at the functional groups (W, U and Z-conformations). Providing a new OPLS-based forcefield parameterization for the critical cyclopropyl group of MAs and extensive simulations in explicit solvents (TIP4P water, hexane), we now present a more complete picture of MA folding properties together with improved simulation analysis techniques. We show that the 'WUZ' distance-based analysis can be used to pinpoint conformers with hairpin bends at the functional groups, with these conformers constituting only a fraction of accessible conformations. Applying principle component analysis (PCA) and refinement using free energy landscapes (FELs), we are able to discriminate a complete and unique set of conformational preferences for representative alpha-, methoxy-and keto-MAs, with overall preference for folded conformations. A control backbone-MA without any mero-chain functional groups showed significantly less folding in the mero-chain, confirming the role of functionalization in directing folding. Keto-MA showed the highest percentage of WUZ-type conformations and, in particular, a tendency to fold at its alpha-methyl trans-cyclopropane group, in agreement with results from Villeneuve et al. MAs demonstrate similar folding in vacuum and water, with a majority of folded conformations around the W-conformation, although the molecules are more flexible in vacuum than in water. Exchange between conformations, with a disperse distribution that includes unfolded conformers, is common in hexane for all MAs, although with more organization for Keto-MA. Globular, folded conformations are newly defined and may be specifically relevant in biofilms.

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Section: Introductionmentioning

confidence: 99%

Revealing solvent-dependent folding behavior of mycolic acids from Mycobacterium tuberculosis by advanced simulation analysis

et al. 2019

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“…Carbon chain lengths are based on results reported by Slama and colleagues. The folding geometry of the mycolic acids is depicted in panel B, as described by Groenewald and colleagues [50], and inspired by the illustration style of Minnikin and colleagues [51].…”

Section: Resultsmentioning

confidence: 99%

SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis

Elghraoui

Modlin

Valafar

2016

Preprint

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The genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of its virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication. Here, we report the assembly and finishing of the H37Ra genome from single-molecule, real-time (SMRT) sequencing. Our assembly reveals that the number of H37Ra-specific variants is less than half of what the Sanger-based H37Ra reference sequence indicates, undermining and, in some cases, invalidating the conclusions of several studies. PE PPE family genes, which are intractable to commonly-used sequencing platforms because of their repetitive and GC-rich nature, are overrepresented in the set of genes in which all reported H37Ra-specific variants are contradicted. We discuss how our results change the picture of virulence attenuation and the power of SMRT sequencing for producing high-quality reference genomes. * Equal contribution † Corresponding author: faramarz@sdsu.edu 1 . CC-BY-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/064840 doi: bioRxiv preprint first posted online Jul. 19, 2016; Tuberculosis is a serious and pervasive public health problem [1]. It is a disease 1 caused by infection of bacteria from the Mycobacterium tuberculosis complex 2 (MTBC). The reference strain, Mycobacterium tuberculosis H37Rv, has an at-3 tenuated counterpart known as H37Ra that is available for studies where facil-4 ities to handle virulent samples are lacking. H37Ra exhibits a distinct colony 5 morphology, an absence of cord formation, decreased resistance to stress and 6 hypoxia, and attenuated virulence in mammalian models [2][3][4]. The H37Ra 22In this study, we sequenced and assembled the genome of M. [14, 15]. This insertion was the heterogeneous inser-56 tion responsible for the discrepant contig ends in our raw genome assembly. 57Such heterogeneity implies either a lack of selection pressure on the insertion in 58 culture, a recent emergence of the insertion, or both. 59The 3456bp insertion in ppe54 with respect to H37RaJH incidentally corre-60 sponds to a tandem duplication of a 1728bp sequence at the same site in H37Rv H37Rv and CDC1551 as "H37Ra-specific". These mutations fall within or ad-95 jacent to (which we term "affecting") 56 genes in H37Rv, which we refer to as The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/064840 doi: bioRxiv preprint first posted online Jul. 19, 2016; colleagues also discovered sequencing errors in the H37Rv reference sequence [5], 98 a number of which were corrected in NC 000962.3 [9], the version used in our 99 study. 100To see how well the HC genes are supported by our assembly of H37Ra, we 101 determined variants with respect to H37Rv ...

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“…This potentially ground breaking result required confirmatory support and this was provided by lipid biomarkers [29]. The mycolic acid profiles were very weak but extremely strong results were recorded for mycocerosates and particularly for mycolipenate, which is found only in members of the M. tuberculosis complex [93]. The combination of lipid biomarkers for the ~17ka bison is summarized in Figure 5.…”

Section: Combined Biomarker Diagnoses-adna and Bacterial Cell Wall LImentioning

confidence: 94%

“…Similarly, the third criterion (3) does not require detailed comment as the "certain techniques" are not specified and the results of any such techniques have nevertheless been peer reviewed and validly published [93,96,106].…”

Section: The Authenticity and Validity Of Adna And Lipid Biomarkers Fmentioning

confidence: 99%

Positive Diagnosis of Ancient Leprosy and Tuberculosis Using Ancient DNA and Lipid Biomarkers

et al. 2017

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Diagnosis of leprosy and tuberculosis in archaeological material is most informative when based upon entire genomes. Ancient DNA (aDNA) is often degraded but amplification of specific fragments also provides reliable diagnoses. Cell wall lipid biomarkers can distinguish ancient leprosy from tuberculosis and DNA extraction residues can be utilized. The diagnostic power of combined aDNA and lipid biomarkers is illustrated by key cases of ancient leprosy and/or tuberculosis. Human tuberculosis was demonstrated in a woman and child from Atlit-Yam (~9 ka) in the Eastern Mediterranean and in the 600 BCE Egyptian "Granville" mummy. Both aDNA and lipids confirmed Pleistocene tuberculosis in a~17 ka bison from Natural Trap Cave, Wyoming. Leprosy is exemplified by cases from Winchester (10th-12th centuries CE) and Great Chesterford (5th-6th centuries CE). A mixed infection from Kiskundorozsma, Hungary (7th century CE) allowed lipid biomarkers to assess the relative load of leprosy and tuberculosis. Essential protocols for aDNA amplification and analysis of mycolic, mycolipenic, mycocerosic acid, and phthiocerol lipid biomarkers are summarized. Diagnoses of ancient mycobacterial disease can be extended beyond the reach of whole genomics by combinations of aDNA amplification and lipid biomarkers, with sole use of the latter having the potential to recognize even older cases.

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Pathophysiological Implications of Cell Envelope Structure in Mycobacterium tuberculosis and Related Taxa

Cited by 30 publications

References 108 publications

Revealing solvent-dependent folding behavior of mycolic acids from Mycobacterium tuberculosis by advanced simulation analysis

Revealing solvent-dependent folding behavior of mycolic acids from Mycobacterium tuberculosis by advanced simulation analysis

SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis

Positive Diagnosis of Ancient Leprosy and Tuberculosis Using Ancient DNA and Lipid Biomarkers

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