Jessica C. Seeliger

Elucidation and Chemical Modulation of Sulfolipid-1 Biosynthesis in Mycobacterium tuberculosis

Background: Sulfolipid-1 (SL-1) is a Mycobacterium tuberculosis outer membrane lipid whose biosynthesis is not fully understood. Results: Chp1 catalyzes two acyl transfer reactions to form SL-1. Sap modulates SL-1 levels and transmembrane transport. Conclusion: The activities of Chp1 and Sap complete the SL-1 pathway. Significance: Lipid biosynthesis and transport are coupled at the membrane interface by multiple proteins that may regulate substrate specificity and flux. Mycobacterium tuberculosis possesses unique cell-surface lipids that have been implicated in virulence. One of the most abundant is sulfolipid-1 (SL-1), a tetraacyl-sulfotrehalose glycolipid. Although the early steps in SL-1 biosynthesis are known, the machinery underlying the final acylation reactions is not understood. We provide genetic and biochemical evidence for the activities of two proteins, Chp1 and Sap (corresponding to gene loci rv3822 and rv3821), that complete this pathway. The membrane-associated acyltransferase Chp1 accepts a synthetic diacyl sulfolipid and transfers an acyl group regioselectively from one donor substrate molecule to a second acceptor molecule in two successive reactions to yield a tetraacylated product. Chp1 is fully active in vitro, but in M. tuberculosis, its function is potentiated by the previously identified sulfolipid transporter MmpL8. We also show that the integral membrane protein Sap and MmpL8 are both essential for sulfolipid transport. Finally, the lipase inhibitor tetrahydrolipstatin disrupts Chp1 activity in M. tuberculosis, suggesting an avenue for perturbing SL-1 biosynthesis in vivo. These data complete the SL-1 biosynthetic pathway and corroborate a model in which lipid biosynthesis and transmembrane transport are coupled at the membrane-cytosol interface through the activity of multiple proteins, possibly as a macromolecular complex.

A riboswitch-based inducible gene expression system for mycobacteria.

Research on the human pathogen Mycobacterium tuberculosis (Mtb) would benefit from novel tools for regulated gene expression. Here we describe the characterization and application of a synthetic riboswitch-based system, which comprises a mycobacterial promoter for transcriptional control and a riboswitch for translational control. The system was used to induce and repress heterologous protein overexpression reversibly, to create a conditional gene knockdown, and to control gene expression in a macrophage infection model. Unlike existing systems for controlling gene expression in Mtb, the riboswitch does not require the co-expression of any accessory proteins: all of the regulatory machinery is encoded by a short DNA segment directly upstream of the target gene. The inducible riboswitch platform has the potential to be a powerful general strategy for creating customized gene regulation systems in Mtb.

Mycobacterial Metabolic Syndrome: LprG and Rv1410 Regulate Triacylglyceride Levels, Growth Rate and Virulence in Mycobacterium tuberculosis.

Mycobacterium tuberculosis (Mtb) mutants lacking rv1411c, which encodes the lipoprotein LprG, and rv1410c, which encodes a putative efflux pump, are dramatically attenuated for growth in mice. Here we show that loss of LprG-Rv1410 in Mtb leads to intracellular triacylglyceride (TAG) accumulation, and overexpression of the locus increases the levels of TAG in the culture medium, demonstrating a role of this locus in TAG transport. LprG binds TAG within a large hydrophobic cleft and is sufficient to transfer TAG from donor to acceptor membranes. Further, LprG-Rv1410 is critical for broadly regulating bacterial growth and metabolism in vitro during carbon restriction and in vivo during infection of mice. The growth defect in mice is due to disrupted bacterial metabolism and occurs independently of key immune regulators. The in vivo essentiality of this locus suggests that this export system and other regulators of metabolism should be considered as targets for novel therapeutics.

Scientists must be taught to manage

Starting an academic lab is like launching a small business. But does scientific training really prepare us for success? As a young investigator just over a year into my job, I feel pressure — much of it self-generated — to produce results, attract funding and ultimately to make a name for myself in my chosen field of bacterial pathogenesis. As researchers, we are trained to work within a rational and methodical framework. But when it comes to running our labs and managing people, we have to rely on our gut feelings, our limited know-how from mentoring a few students or our observations of our previous advisers. We can often feel ill-prepared. Take dealing with a difficult co-worker or motivating students. As scientists, we must be honest with someone about faults in data or reasoning. But while striving for this scientific objectivity, we can forget the importance of body language and of directing discussion at a problem rather than a person. And even something as apparently straightforward as having a meeting can be problematic. The many collective hours spent around conference tables can feel like lost time when agendas wander and goals are not met. Would we do any better if we received formal training that gave us a logical framework for lab management? Some young investigators would no doubt argue that such training is inefficient and ineffective. The classic method is to work from your own experience in your mentors’ labs. Although this is a valuable starting point, building a new lab and serving as its sole head is a very different prospect from working in an established lab with senior students and support staff. So my current support network consists mainly of a handful of other young investigators, all of us amazed by the universality of the challenges we face. We trade tips and anecdotes about recruiting and retaining, motivating and negotiating, and we agonize over mistakes. So, we need help — or at least, some of us do. Yet funding agencies offer no routine management training for people at my level. This is despite the many career-progression programmes and workshops now available for graduate students and postdocs. The Burroughs Wellcome Fund and Howard Hughes Medical Institute did create a course for people at my stage of a scientific career, called ‘Making the Right Moves’. But the course ran only twice — in 2002 and 2005. What endures is a book based on the course, which, along with Kathy Barker’s At the Helm and Lab Dynamics by Carl Cohen and Suzanne Cohen, constitutes almost the entire reference library available to new investigators. Recognition of this training void has come recently from an unexpected corner: the American Express Foundation, which last year started to fund an annual ‘Workshop on Leadership in BioScience’ at Cold Spring Harbor Laboratory in New York. Last month I went on the course, alongside my husband — Markus Seeliger, also a young investigator — and 25 scientists from around the world at a similar stage of their careers, for three days of lectures, role-playing exercises and case studies. Everyone has their own story of poor management. The major advantage of the workshop we attended was that it was away from our home university, so that we could discuss sensitive personal situations in confidence. Some of the toughest problems are those that you might not feel comfortable about discussing with your principal investigator, your mentor or your chair. We practised the difficult issues — how to manage meetings, for example, from distributing the agenda in advance and keeping everyone on task, to ending on a note of consensus. And through role plays, we learned how to structure negotiations as a problem-solving process rather than a battle of wills. Except in cases of misconduct, criticism need not be personal, particularly when one is trying to motivate students. Being honest does not mean that one need be brusque or unsympathetic; we can preserve scientific integrity and encourage trainees positively. I would strongly recommend such training. And although it is useful for postdocs, it is more crucial for young faculty members. The workshop was appealing because it was tailored to our situations by people familiar with both the academic domain and the biotech world, where such training is more common. Academic institutions must recognize the value of this pioneering effort and support or create such programmes for their own faculty members. They make multimillion-dollar investments in us, and, to protect their interests, should invest as seriously in leadership skills as in the progress of science. I am already using what I learned. When I notice that I am dominating group discussions, for instance, I try to be more patient and to allow others to consider and voice their opinions. I like to think that, as a result, quieter members of my lab are becoming more confident, and that we all benefit from increased intellectual exchange. My husband has put the ideas into practice too: we wrote this article together, but were then told we could put only one name on it. Luckily, the workshop covered how to resolve authorship disputes. ■

The rv1184c Locus Encodes Chp2, an Acyltransferase in Mycobacterium tuberculosis Polyacyltrehalose Lipid Biosynthesis

Trehalose glycolipids are found in many bacteria in the suborder Corynebacterineae, but methyl-branched acyltrehaloses are exclusive to virulent species such as the human pathogen Mycobacterium tuberculosis. In M. tuberculosis, the acyltransferase PapA3 catalyzes the formation of diacyltrehalose (DAT), but the enzymes responsible for downstream reactions leading to the final product, polyacyltrehalose (PAT), have not been identified. The PAT biosynthetic gene locus is similar to that of another trehalose glycolipid, sulfolipid 1. Recently, Chp1 was characterized as the terminal acyltransferase in sulfolipid 1 biosynthesis. Here we provide evidence that the homologue Chp2 (Rv1184c) is essential for the final steps of PAT biosynthesis. Disruption of chp2 led to the loss of PAT and a novel tetraacyltrehalose species, TetraAT, as well as the accumulation of DAT, implicating Chp2 as an acyltransferase downstream of PapA3. Disruption of the putative lipid transporter MmpL10 resulted in a similar phenotype. Chp2 activity thus appears to be regulated by MmpL10 in a relationship similar to that between Chp1 and MmpL8 in sulfolipid 1 biosynthesis. Chp2 is localized to the cell envelope fraction, consistent with its role in DAT modification and possible regulatory interactions with MmpL10. Labeling of purified Chp2 by an activity-based probe was dependent on the presence of the predicted catalytic residue Ser141 and was inhibited by the lipase inhibitor tetrahydrolipstatin (THL). THL treatment of M. tuberculosis resulted in selective inhibition of Chp2 over PapA3, confirming Chp2 as a member of the serine hydrolase superfamily. Efforts to produce in vitro reconstitution of acyltransferase activity using straight-chain analogues were unsuccessful, suggesting that Chp2 has specificity for native methyl-branched substrates.

Transport of outer membrane lipids in mycobacteria

The complex organization of the mycobacterial cell wall poses unique challenges for the study of its assembly. Although mycobacteria are classified evolutionarily as Gram-positive bacteria, their cell wall architecture more closely resembles that of Gram-negative organisms. They possess not only an inner cytoplasmic membrane, but also a bilayer outer membrane that encloses an aqueous periplasm and includes diverse lipids that are required for the survival and virulence of pathogenic species. Questions surrounding how mycobacterial outer membrane lipids are transported from where they are made in the cytoplasm to where they function at the cell exterior are thus similar, and similarly compelling, to those that have driven the study of Gram-negative outer membrane transport pathways. However, little is understood about these processes in mycobacteria. Here we contextualize these questions by comparing our current knowledge of mycobacteria with better-defined systems in other organisms. Based on this analysis, we propose possible models and highlight continuing challenges to improving our understanding of outer membrane assembly in these medically and environmentally important bacteria. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.

Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids.

Although they are classified as Gram-positive bacteria, Corynebacterineae possess an asymmetric outer membrane that imparts structural and thereby physiological similarity to more distantly related Gram-negative bacteria. Like lipopolysaccharide in Gram-negative bacteria, lipids in the outer membrane of Corynebacterineae have been associated with the virulence of pathogenic species such as Mycobacterium tuberculosis (Mtb). For example, Mtb strains that lack long, branched-chain alkyl esters known as dimycocerosates (DIMs) are significantly attenuated in model infections. The resultant interest in the biosynthetic pathway of these unusual virulence factors has led to the elucidation of many of the steps leading to the final esterification of the alkyl β-diol, phthiocerol, with branched-chain fatty acids known as mycocerosates. PapA5 is an acyltransferase implicated in these final reactions. Here, we show that PapA5 is indeed the terminal enzyme in DIM biosynthesis by demonstrating its dual esterification activity and chain-length preference using synthetic alkyl β-diol substrate analogues. By applying these analogues to a series of PapA5 mutants, we also revise a model for the substrate binding within PapA5. Finally, we demonstrate that the Mtb Ser/Thr kinases PknB and PknE modify PapA5 on three overlapping Thr residues and that a fourth Thr is unique to PknE phosphorylation. These results clarify the DIM biosynthetic pathway and indicate post-translational modifications that warrant further elucidation for their roles in the regulation of DIM biosynthesis.

Monstrous Mycobacterial Lipids

When it comes to lipid diversity, no bacterial genus approaches Mycobacterium. In this issue of Cell Chemical Biology, Burbaud et al. (2016) provide a multi-genic working model for the biosynthesis of trehalose polyphleate (TPP), one of the largest known lipids in mycobacteria. They demonstrate that this lipid is made by diverse mycobacterial species, including those of medical importance.

Using Riboswitches to Regulate Gene Expression and Define Gene Function in Mycobacteria

Mycobacteria include both environmental species and many pathogenic species such as Mycobacterium tuberculosis, an intracellular pathogen that is the causative agent of tuberculosis in humans. Inducible gene expression is a powerful tool for examining gene function and essentiality, both in in vitro culture and in host cell infections. The theophylline-inducible artificial riboswitch has recently emerged as an alternative to protein repressor-based systems. The riboswitch is translationally regulated and is combined with a mycobacterial promoter that provides transcriptional control. We here provide methods used by our laboratory to characterize the riboswitch response to theophylline in reporter strains, recombinant organisms containing riboswitch-regulated endogenous genes, and in host cell infections. These protocols should facilitate the application of both existing and novel artificial riboswitches to the exploration of gene function in mycobacteria.

Characterization of engineered preQ1 riboswitches for inducible gene regulation in mycobacteria

We report here the behavior of naturally occurring and rationally engineered preQ1 riboswitches and their application to inducible gene regulation in mycobacteria. Because mycobacteria lack preQ1 biosynthetic genes, we hypothesized that preQ1 could be used as an exogenous nonmetabolite ligand to control riboswitches in mycobacteria. Selected naturally occurring preQ1 riboswitches were assayed and successfully drove preQ1-dependent repression of a green fluorescent protein reporter in Mycobacterium smegmatis Using structure-based design, we engineered three preQ1 riboswitches from Thermoanaerobacter tencongensis, Bacillus subtilis, and Lactobacillus rhamnosus toward achieving higher response ratios and increased repression. Assuming a steady-state model, variants of the T. tencongensis riboswitch most closely followed the predicted trends. Unexpectedly, the preQ1 dose response was best described by a model with a second, independent preQ1 binding site. This behavior was general to the preQ1 riboswitch family, since the wild type and rationally designed mutants of riboswitches from all three bacteria behaved analogously. Across all variants, the response ratios, which describe expression in the absence versus the presence of preQ1, ranged from <2 to ∼10, but repression in all cases was incomplete up to 1 mM preQ1. By reducing the transcript expression level, we obtained a preQ1 riboswitch variant appropriate for inducible knockdown applications. We further showed that the preQ1 response is reversible, is titratable, and can be used to control protein expression in mycobacteria within infected macrophages. By engineering naturally occurring preQ1 riboswitches, we have not only extended the tools available for inducible gene regulation in mycobacteria but also uncovered new behavior of these riboswitches.IMPORTANCE Riboswitches are elements found in noncoding regions of mRNA that regulate gene expression, typically in response to an endogenous metabolite. Riboswitches have emerged as important tools for inducible gene expression in diverse organisms. We noted that mycobacteria lack the biosynthesis genes for preQ1, a ligand for riboswitches from diverse bacteria. Predicting that preQ1 is not present in mycobacteria, we showed that it controls optimized riboswitches appropriate for gene knockdown applications. Further, the riboswitch response is subject to a second independent preQ1 binding event that has not been previously documented. By engineering naturally occurring riboswitches, we have uncovered a new behavior, with implications for riboswitch function in its native context, and extended the tools available for inducible gene regulation in mycobacteria.