Recent Insights into the Structure and Function of Mycobacterial Membrane Proteins Facilitated by Cryo-EM

Abstract

Abstract

Mycobacterium tuberculosis (Mtb) is one of the deadliest pathogens encountered by humanity. Over the decades, its characteristic membrane organization and composition have been understood. However, there is still limited structural information and mechanistic understanding of the constituent membrane proteins critical for drug discovery pipelines. Recent advances in single-particle cryo-electron microscopy and cryo-electron tomography have provided the much-needed impetus towards structure determination of several vital Mtb membrane proteins whose structures were inaccessible via X-ray crystallography and NMR. Important insights into membrane composition and organization have been gained via a combination of electron tomography and biochemical and biophysical assays. In addition, till the time of writing this review, 75 new structures of various Mtb proteins have been reported via single-particle cryo-EM. The information obtained from these structures has improved our understanding of the mechanisms of action of these proteins and the physiological pathways they are associated with. These structures have opened avenues for structure-based drug design and vaccine discovery programs that might help achieve global-TB control. This review describes the structural features of selected membrane proteins (type VII secretion systems, Rv1819c, Arabinosyltransferase, Fatty Acid Synthase, F-type ATP synthase, respiratory supercomplex, ClpP1P2 protease, ClpB disaggregase and SAM riboswitch), their involvement in physiological pathways, and possible use as a drug target.

Graphic Abstract

Tuberculosis is a deadly disease caused by Mycobacterium tuberculosis. The Cryo-EM and tomography have simplified the understanding of the mycobacterial membrane organization. Some proteins are located in the plasma membrane; some span the entire envelope, while some, like MspA, are located in the mycomembrane. Cryo-EM has made the study of such membrane proteins feasible.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00232-021-00179-w.

Introduction

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB)—a disease that costs as many as 200,000 deaths per year worldwide, and almost a quarter of the world population is infected with it (Gaensbauer and Broadhurst 2019). Even after decades of research, there still is a lack of an effective short treatment course or a potent vaccine and better diagnostics. Due to non-compliance with the drug regimen, a high percentage of TB patients drop-out from the treatment program that lasts at least 6 months in general (Awofeso 2008; Churchyard 2018). This high-dropout rate has led to increased cases of TB relapse and drug resistance, making TB even more challenging to treat. Although new drugs have been introduced, none of them have proven to be completely effective. The only notable exception is the use of Pretomanid in combination with Bedaquiline (BDQ) and Linezolid for the treatment of a specific type of highly treatment-resistant TB of the lungs that has shown promise (Bigelow et al. 2020).

Given the current situation, the World Health Organization’s (WHO) ‘End the TB’ strategic program that aims to reduce TB incidences by 80% and deaths by 90% by the year 2030 seems rather ambitious (World Health Organization 2020). The ongoing COVID-19 pandemic has made the situation even more challenging (Grüber 2020) by severely disrupting the TB, Human Immunodeficiency Virus (HIV), and Malaria programs worldwide. In addition, according to recent estimates, COVID-19 has set back worldwide TB treatment efforts by almost a decade and reducing gains to control the disease (The Global Fund 2020). Under such circumstances, we are in urgent need of effective treatment for TB.

A deep understanding of the mechanism of action and atomic details of critical elements contributing to any pathogenic micro-organism's virulence is crucial for successful and effective drug development. The mycobacterial membrane enables the bacilli to survive in the hostile environment inside the host (Lin et al. 2002; Hahn et al. 2005; McClean 2012). The characteristic cell envelope, slow growth rate and unique metabolic features (e.g. glyoxalate pathway, diauxic growth, etc.) of Mtb make it an exciting but challenging system to study (Faller et al. 2004; Målen et al. 2011; Koul et al. 2014). The Mtb cell wall has a distinctive composition, and despite close resemblance with Gram-positive bacteria, its outer membrane contains a complex mixture of lipids such as mycolic acids that distinguishes it from other bacteria (Marrakchi et al. 2014). An extensive physicochemical and structural characterization of Mtb membrane samples could help us understand its composition. Further, various ‘omics’ studies have revealed information about constituent membrane proteins and the secretome of the pathogen. However, there is a large gap in the understanding of the Mtb membrane proteins from their structural point of view. This has been a significant bottleneck in deciphering the roles and mechanism of action of these proteins, which in turn has thwarted the discovery and development of novel therapeutics.

Cryo-electron microscopy (cryo-EM) is proving instrumental in breaking this bottleneck (Munir et al. 2021). Recent advances in cryo-EM have been the silver lining and have proven to be extremely helpful in unraveling the structures of key drug targets of various pathogens, including Mtb. A relatable example has been structure elucidation of various membrane proteins and drug targets of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in record time. This has advanced drug discovery and vaccine development efforts against SARS-CoV-2 worldwide (Jeong et al. 2020; Wrapp et al. 2020). Not surprisingly, cryo-EM has also helped determine structures of key Mtb proteins that are important for virulence and survival of the pathogen and are important targets for drug discovery and vaccine development programs. Furthermore, developments in cryo-electron tomographic (cryo-ET) techniques and cryo-EM have contributed a tremendous amount of structural knowledge about mycobacterial membrane organization and its constituent membrane proteins. This has proven instrumental in modern drug discovery and a better understanding of host–pathogen interactions (Sani et al. 2010b). So far, 75 cryo-EM structures of mycobacterial proteins have been deposited in the Protein data bank (PDB) (Table 1) (Burley et al. 2019). The majority of these structures are membrane proteins. However, very few of these have been tested as targets for drug discovery, while others are yet to be explored. In this review, we discuss the structures of some of the key Mtb proteins and protein complexes elucidated by EM. The list includes cryo-EM structures of type VII secretion systems, Rv1819c, Arabinosyltransferase, Fatty Acid Synthase (FAS), F-type ATP synthase, respiratory supercomplex, Caseinolytic proteases (Clp) P1P2 protease, ClpB disaggregase and S-adenosylmethionine (SAM) riboswitch proteins-protein complexes. These proteins-protein complexes are involved in distinct and vital cellular processes like transport, virulence, electron transport, etc., in Mtb and are promising candidates for drug development. These cryo-EM structures have opened new avenues for novel drug discovery programs. In addition, how recent advents in cryo-EM have helped us in gaining insights into the Mtb membrane organization is briefly discussed. Compiled structural information about mycobacterial membrane and membrane proteins deduced using cryo-EM would provide the researchers with a visual picture of reaction mechanisms associated with them and help design novel antituberculars.

Table 1.

List of mycobacterial membrane protein structures determined using cryo-EM and deposited in PDB (The titles are as deposited by respective authors)

Sr. no	PDB code	Title of the PDB Entry	References
1	5V93	Cryo-EM structure of the 70S ribosome from M. tuberculosis bound with Capreomycin	Yang et al. (2017)
2	5ZEP	M. Smegmatis hibernating state 70S ribosome structure	Mishra et al. (2018)
3	6DZI	Cryo-EM Structure of M. Smegmatis 70S C(minus) ribosome 70S-MPY complex	Li et al. (2018a)
4	5ZEB	M. Smegmatis P/P state 70S ribosome structure	Mishra et al. (2018)
5	5V7Q	Cryo-EM structure of the large ribosomal subunit from M. tuberculosis bound with a potent linezolid analog	Yang et al. (2017)
6	5ZET	M. smegmatis P/P state 50S ribosomal subunit	Mishra et al. (2018)
7	6DZP	Cryo-EM Structure of M. smegmatis C(minus) 50S ribosomal subunit	Li et al. (2018a)
8	6DZK	Cryo-EM Structure of M. smegmatis C(minus) 30S ribosomal subunit with MPY	Li et al. (2018a)
9	5XYM	Large subunit of M. smegmatis ribosome	Li et al. (2018b)
10	5XYU	Small subunit of M. smegmatis ribosome	Li et al. (2018b)
11	5ZEU	M. smegmatis P/P state 30S ribosomal subunit	Mishra et al. (2018)
12	5O61	The complete structure of the M. smegmatis 70S ribosome	Hentschel et al. (2017)
13	5O60	50S large ribosomal subunit from M. smegmatis	Hentschel et al. (2017)
14	5O5J	30S small ribosomal subunit from M. smegmatis	Hentschel et al. (2017)
15	6EDT	M. tuberculosis RNAP open promoter complex with RbpA/CarD and AP3 promoter	Boyaci et al. (2019)
16	6EE8	M. tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter	Boyaci et al. (2019)
17	6EEC	M. tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter captured by Corallopyronin	Boyaci et al. (2019)
18	6C04	M. tuberculosis RNAP Holo/RbpA/double fork DNA -closed clamp	Boyaci et al. (2018)
19	6BZO	M. tuberculosis RNAP Holo/RbpA/Fidaxomicin/upstream fork DNA	Boyaci et al. (2018)
20	6FBV	M. tuberculosis RNA polymerase in complex with Fidaxomicin	Lin et al. (2018)
21	6HWH	Functional obligate respiratory supercomplex from M. smegmatis	Wiseman et al. (2018)
22	6C06	M. tuberculosis RNAP Holo/RbpA/Fidaxomicin	Boyaci et al. (2018)
23	6C05	M. tuberculosis RNAP Holo/RbpA in relaxed state	Boyaci et al. (2018)
24	6M7J	M. tuberculosis RNAP with RbpA/us fork and Corallopyronin	Boyaci et al. (2019)
25	5LZP	Binding of the C-terminal GQYL motif of the bacterial proteasome activator Bpa to the 20S proteasome	Bolten et al. (2016)
26	7BVF	Cryo-EM structure of M. tuberculosis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol	Zhang et al. (2020b)
27	6SGZ	M. smegmatis Structure of protomer 2 of the ESX-3 core complex	Famelis et al. (2019)
28	6SGX	M. smegmatis Structure of protomer 1 of the ESX-3 core complex	Famelis et al. (2019)
29	6SGW	M. smegmatis Structure of the ESX-3 core complex	Famelis et al. (2019)
30	6BGL	Doubly PafE-capped 20S core particle in M. tuberculosis	Hu et al. (2018)
31	6BGO	Singly PafE-capped 20S CP in M. tuberculosis	Hu et al. (2018)
32	6EYD	M. smegmatis RNA polymerase Sigma-A holoenzyme	Kouba et al. (2019)
33	6UMM	M. smegmatis ESX-3 translocon complex	Poweleit et al. (2019)
34	6F6W	Structure of M. smegmatis RNA polymerase core	Kouba et al. (2019)
35	7BVC	M. smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol	Zhang et al. (2020b)
36	7BVG	M. smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose	Zhang et al. (2020b)
37	7BX8	M. smegmatis arabinosyltransferase complex EmbB2-AcpM2 in symmetric "resting state"	Zhang et al. (2020a)
38	7BWR	M. smegmatis arabinosyltransferase complex EmbB2-AcpM2 in substrate DPA bound asymmetric "active state"	Zhang et al. (2020a)
39	6VGQ	ClpP1P2 complex from M. tuberculosis with GLF-CMK bound to ClpP1	Vahidi et al. (2020)
40	6VGK	ClpP1P2 complex from M. tuberculosis	Vahidi et al. (2020)
41	6VGN	ClpP1P2 complex from M. tuberculosis bound to ADEP	Vahidi et al. (2020)
42	7BVE	M. smegmatis arabinosyltransferase EmbC2-AcpM2 in complex with ethambutol	Zhang et al. (2020b)
43	3J83	M. tuberculosis Heptameric EspB Rosetta model	Solomonson et al. (2015)
44	5ZEY	M. smegmatis Trans-translation state 70S ribosome	Mishra et al. (2018)
45	6SGY	Structure of EccB3 dimer from the ESX-3 core complex	Famelis et al. (2019)
46	6GJC	Structure of M. tuberculosis Fatty Acid Synthase—I	Elad et al. (2018)
47	4V8V	M. tuberculosis fatty acid synthase multienzyme complex	Ciccarelli et al. (2013)
48	4V8W	M. tuberculosis fatty acid synthase multienzyme complex	Ciccarelli et al. (2013)
49	6ED3	M. tuberculosis ClpB in complex with AMPPNP	Yu et al. (2018)
50	6PPU	Cryo-EM structure of AdnAB-AMPPNP-DNA complex	Jia et al. (2019)
51	6DJU	M. tuberculosis ClpB in complex with ATPgammaS and casein, Conformer 1	Yu et al. (2018)
52	6DJV	M. tuberculosis ClpB in complex with ATPgammaS and casein, Conformer 2	Yu et al. (2018)
53	6PPR	Cryo-EM structure of AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and DNA	Jia et al. (2019)
54	6WBY	Single-Particle Cryo-EM Structure of Arabinofuranosyltransferase AftD from Mycobacteria, Mutant R1389S Class 2	Tan et al. (2020b)
55	6WBX	Single-Particle Cryo-EM Structure of Arabinofuranosyltransferase AftD from Mycobacteria, Mutant R1389S Class 1	Tan et al. (2020b)
56	6TQF	The structure of ABC transporter Rv1819c in AMPPNP bound state	Rempel et al. (2020)
57	6TQE	The structure of ABC transporter Rv1819c without addition of substrate	Rempel et al. (2020)
58	6UES	Apo SAM-IV Riboswitch	Zhang et al. (2019b)
59	6PPJ	Cryo-EM structure of AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP	Jia et al. (2019)
60	4V8L	M. smegmatis Fatty Acid Synthase	Boehringer et al. (2013)
61	6UET	SAM-bound SAM-IV riboswitch	Zhang et al. (2019b)
62	6W98	Single-Particle Cryo-EM Structure of Arabinofuranosyltransferase AftD from Mycobacteria	Tan et al. (2020b)
63	6ADQ	Respiratory Complex CIII2CIV2SOD2 from M. smegmatis	Gong et al. (2018)
64	2BYU	M.tuberculosis Acr1(Hsp 16.3) fitted with wheat sHSP dimer	Kennaway et al. (2005)
65	6X0O	Cryo-EM structure of M. tuberculosis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol	Tan et al. (2020a)
66	6XZC	CryoEM structure of the ring-shaped virulence factor EspB from M. tuberculosis	Korotkova et al. (2015)
67	6LUM	Structure of M. smegmatis succinate dehydrogenase 2	Not published
68	7JG5	Cryo-EM structure of bedaquiline-free M. smegmatis ATP synthase rotational state 1	Guo et al. (2020a)
69	7JG6	Cryo-EM structure of bedaquiline-free M. smegmatis ATP synthase rotational state 2 (backbone model)	Guo et al. (2020a)
70	7JG7	Cryo-EM structure of bedaquiline-free M. smegmatis ATP synthase rotational state 3 (backbone model)	Guo et al. (2020a)
71	7JG8	Cryo-EM structure of bedaquiline-saturated M. smegmatis ATP synthase rotational state 1 (backbone model)	Guo et al. (2020a)
72	7JG9	Cryo-EM structure of bedaquiline-saturated M. smegmatis ATP synthase rotational state 2 (backbone model)	Guo et al. (2020a)
73	7JGA	Cryo-EM structure of bedaquiline-saturated M. smegmatis ATP synthase rotational state 3	Guo et al. (2020a)
74	7JGB	Cryo-EM structure of bedaquiline-free M. smegmatis ATP synthase FO region	Guo et al. (2020a)
75	7JGC	Cryo-EM structure of bedaquiline-saturated M. smegmatis ATP synthase FO region	Guo et al. (2020a)

Cryo-Electron Tomography and Mycobacterial Membrane Organization

The mycobacterial cell wall is a unique structure that acts as a permeability barrier, and it is essential for survival, virulence, and pathogenesis (Barry Iii et al. 1998; Etienne et al. 2002). Over the decades, researchers have been trying to elucidate the mycobacterial membrane structure using transmission electron microscopy. However, sample preparation methods that involved fixing with various solvents and staining with heavy metal salts in different labs led to imaging of dehydrated membranes (Daffe and Draper 1997). The information obtained from these studies thus suffered from sample preparation artifacts along with lack of details (Paul and Beveridge 1992; Zuber et al. 2008). Advances in sample preparation methods, specially CEMOVIS (Al-Amoudi et al. 2004; Hoffmann et al. 2008) and cryo-EM of the mycobacterial capsular layer (Sani et al. 2010a), have allowed the visualization of fully hydrated and unstained mycobacterial membrane providing new structural insights into membrane organization. This unique combination of CEMOVIS and cryo-ET of plunge frozen membranes has provided an improved understanding of the structure of lipid bilayer and the outer membrane (Hoffmann et al. 2008).

Summing up the information available, the four-layered envelope of Mtb is about 75–80-nm-thick and can be described from the exterior to the interior of the cell (Daffé and Marrakchi 2019). A capsule layer of ~ 35 nm thickness is associated with ~ 8 nm outer membrane made up of mycolipids. The outer membrane is, in turn, linked to a ~ 35 nm thick cell wall primarily made up of the arabinogalactan layer tethered to the peptidoglycan layer (Alsteens et al. 2008). This is followed by a periplasmic space and ~ 7 nm thick granular layer tethered to the cell's plasma membrane (Lee et al. 2005), where membrane proteins are embedded (Besra and Chatterjee 1994). Interestingly, about thirteen enzymes are involved in synthesizing the arabinogalactan-peptidoglycan complex, which are unique to Mycobacteria (Lee et al. 2005; Crick and Brennan 2008) and hence are putative drug targets against Mtb.

While the understanding of Mtb cell envelops has improved due to their imaging in cryo-conditions, the resolutions achieved are still low. Moreover, it has been shown that lab-grown bacteria may have compositional heterogeneity in the membrane due to the kind of media used (Sani et al. 2010a) or the presence of detergents that may lead to capsule shedding (Hoffmann et al. 2008; Sani et al. 2010a). These problems may be overcome by cryo-EM of vitrified Mtb engulfed by macrophages. However, these are usually too thick to be vitrified properly. The recent developments in sample vitrification methods, high-pressure freezing, and preparation of thin lamella suitable for cryo-EM via FIB-SEM may make it possible (Gorelick et al. 2019; Ravelli et al. 2020). Besides, advances in cryo-ET and the establishment of unique Biosafety Level–3 cryo-EM facilities have raised the hopes of carrying out an exhaustive and detailed structural characterization of native Mtb envelop and membranes (Parvate 2018).

Cryo-EM Structures of Mtb Membrane Proteins

The majority of membrane proteins are recalcitrant to crystallization. Thus, several key Mtb membrane protein structures could not be determined by X-ray crystallography, severely impacting the progress of the Mtb drug discovery field. One of the key issues had been the requirement of milligram quantities of highly pure, compositionally, and conformationally homogenous protein sample for crystallization (Acharya and Lloyd 2005). Moreover, most Mtb membrane proteins express poorly in recombinant expression systems and require extensive optimization of expression and purification conditions (Korepanova et al. 2007). Unlike cytosolic proteins, membrane proteins are highly unstable when extracted from the lipid bilayer (Haltia and Freire 1995). Therefore, to mimic such an environment, detergents/lipids are added to the sample during membrane protein extraction and purification. Due to the presence of lipids/detergents, crystallization becomes more difficult. Technological advancements in cryo-EM, such as the development of direct electron detectors and stable microscopes, have proven beneficial for protein structure determination, especially for membrane proteins (Frank 2017). It overcomes the above two limitations as it requires less amount of sample and does not require crystallization (Renaud et al. 2018). By overcoming these two significant barriers, cryo-EM has accelerated the membrane protein structure determination.

Cryo-EM single-particle analysis technique has led to the structure determination of several essential Mtb proteins providing novel structural and mechanistic insights into their functions. We discuss some of the protein–protein complexes that are therapeutically important targets and whose structures were recently solved in a near-native environment due to current advances in the cryo-EM technique.

Structural Insights into Mycobacterial Secretion Systems and Transporters

ESX/ Type VII Secretion System

Bacterial cell membranes contain specific protein complexes used by the pathogenic bacteria to secrete virulence factors helping them to invade the host. Such secretion systems are classified into different types (e.g., Type I, Type II,…Type IX) based on their structure, composition, and function (Green and Mecsas 2016; Lasica et al. 2017). Mycobacteria consist of five paralogous ESX (ESX: ESAT-6 Secretion System, ESAT-6: 6 kDa early secretory antigenic target) secretion systems important for virulence, immune modulation, gene transfer, nutrient and metabolite uptake, and cell physiology of the bacterium (Bunduc et al. 2020). These systems release certain effectors, commonly known as virulence factors, that help the Mtb infect the host. It is proven that the mycobacterial cytosolic translocation is mediated via ESAT-6, a secretion product of the ESX-1 secretion system, and established a connection between the translocation of pathogenic mycobacterium and its virulence (Houben et al. 2012). Although the role of effector proteins from ESX-1, 3, and 5 systems have been traced, the lack of three-dimensional structure of the ESX system had limited the knowledge of its mechanism of operation until the structure of ESX-3 from M. smegmatis was solved at ~ 4 Å via EM (Famelis et al. 2019). During the limited supply of iron, ESX-3 is expressed (Rodriguez et al. 2002; Macikag et al. 2009) and is reported to be associated with various functions such as metal ion homeostasis (Serafini et al. 2009; Siegrist et al. 2009; Tinaztepe et al. 2016; Tufariello et al. 2016), repair of phagosomal damage, and phagosome maturation (Mehra et al. 2013; Portal-Celhay et al. 2016; Mittal et al. 2018).

The ESX-3 secretion system consists of core components called 'ESC conserved component,' (Ecc) i.e., Ecc viz; EccB, EccC, EccD, EccE, and fifth component MycP. These components are responsible for releasing virulence factors EsxA and EsxB (Abdallah et al. 2006; Brodin et al. 2006; Ohol et al. 2010; Sloan Siegrist et al. 2014; Ates et al. 2015; Van Winden et al. 2016). The Ecc components together form a hexameric pore in its cell envelope. This pore releases virulence factors that help them infect the host and evade the actions of the host immune system. The membrane-anchored element ‘MycP’ possesses protease activity, while the fork domain of EccB is towards the periplasmic face (Fig. 1a1). The ESX-3 complex is made up of two protomers. Each protomer constitutes EccB3, EccC3, and EccE3 as a single copy and EccD3 in two copies of homo-dimers. The EccB3 from each protomer is attached to a transmembrane helix (TMH) that anchors it firmly within two protomers and holds the two protomers together with the help of the fork domain (Fig. 1a2). Together, these two protomers form the secretion pore with dimensions large enough to transport dimeric substrate proteins in folded conformation across its cell envelope. Another structure resolved at 3.7 Å, has elaborated how the pseudo-ATPase domain (reconstructed at ~ 10 Å) in the translocation gate is positioned in the EccC3 domain towards the cytoplasm (Poweleit et al. 2019).

Fig. 1.

a1 Structure of EccB dimer from the ESX-3 core complex showing fork architecture at the periplasm (PDB: 6SGY). a2 The ESX-3 core complex structure formed by EccC, EccD, and EccE subunits is arranged laterally. The pale green box is the trans-membrane region. The translocon pore is formed by the EccD subunit (PDB: 6SGW). b The structure of ABC transporter Rv1819c. In the inset, the binding site for the nucleotide (PDB: 6TQE) is shown. The substrate enters from the cap end of the transporter. The conversion of ATP to ADP leads to the import of the incoming substrate from the NBD end (Color figure online)

The structure of ESX-1 secretion associated protein B (EspB), a secretion protein was also predicted from a cryo-ET, with a resolution of about 30 Å from Mtb (Solomonson et al. 2015). It confers sevenfold symmetry with approximate dimensions of 100 Å × 80 Å cylinders with about 50 Å pore. It has been reported that EspB C-terminal domain (CTD) is processed by the membrane-bound protease MycP1P2 following secretion (McLaughlin et al. 2007; Xu et al. 2007; Ohol et al. 2010; Solomonson et al. 2013; Wagner et al. 2013). A visual snapshot of mycobacterial membrane organization using electron microscopy with proteomic confirmation of the presence of ESX-1-secreted proteins has been reported (Sani et al. 2010b). Moreover, an EM structure of ESX-1 secreted Mtb-EspB has been reconstructed at 3.37 Å resolution providing important structural and functional insights. The seven units of EspB form a heptameric cylinder with dimensions of 90 Å × 90 Å. The central channel pore is about 45 Å wide. The overall cylindrical arrangement of EspB indicates that it could facilitate the transport of ESX-1 substrates such as EsxA-EsxB or B form DNA molecules (Korotkova et al. 2015). The ESX-3 is proven to be indispensable for Zinc and iron metabolism in Mtb. BBH7, a benzyloxybenzylidene-hydrazine compound, has been identified as an inhibitor of the ESX system, which induces Zinc stress in Mtb, thereby severely inhibiting bacterial growth (Rybniker et al. 2014; Cole 2016). Combining the structural information with the knowledge of inhibitors like BBH7, highly specific inhibitors against ESX systems could be designed that may reduce the virulence of Mtb and thus could be an effective alternative antitubercular strategy.

Rv1819c, an ABC Transporter

The ATP-binding cassette transporters (ABC transporters) are probably one of the most studied superfamilies of the multi-subunit transporters, which transport a broad spectrum of molecules at the expense of ATP (Choudhuri et al. 2002). The presence of membrane-spanning domains (MSD) and the nucleotide-binding domains (NBD) is typical of ABC transporters. The ATPase activity is associated with the NBD, which is positioned towards the cytoplasm. ATP hydrolysis provides the energy required to transport substrates across membranes (De Rossi et al. 2006). The gene rv1819c was shown to be associated with the uptake/transport of cobalamin in Mycobacteria (Gopinath et al. 2013). However, the protein Rv1819c was related to the transport of antimicrobial peptides like Bleomycin (Domenech et al. 2009) and efflux of antibiotic ciprofloxacin when expressed in C. glutamicum, indicating its potential role in providing resistance through drug efflux (Mazando et al. 2013).

Recently, the structure of the Rv1819c homodimer in the nucleotide bound state was determined at 3.5 Å resolution using cryo-EM (Rempel et al. 2020). The electron density for detergent micelles, observed in the cryo-EM map, helped approximate membrane position around the protein. The structure also revealed the presence of an ABC exporter fold in Rv1819c. The characteristic features in this fold that distinguish it from the similar fold found in previously reported ABC transporters are the unusually large hydrophilic cavity and an additional TMH-0 towards the N-terminal (Korkhov et al. 2012; Choudhury et al. 2014; Lin et al. 2015). The cavity volume measures about 7,700 ų spanning almost the entire width of the lipid bilayer membrane. It is made up of two lateral chambers, larger across the membrane, while a smaller one acts as a junction between the larger chamber and the NBD (Fig. 1b). The structures also revealed a 17 amino acid residues long loop in TMH3, constricting between the two chambers near the membrane towards the cytoplasm. The cavity's inner side is lined by the network of polar and negatively charged amino acid residues. Such a lining could facilitate the exchange of hydrophilic molecules across the cavity, thus in and out of the membrane. Considering the cavity volume, it could facilitate the transport of peptides, too, as seen in transporters of Microcin-J25 export ATP-binding/permease protein McjD and the peptidase-containing ATP-binding cassette transporters (PCAT) (Choudhury et al. 2014; Lin et al. 2015). Further, the structure shows that the exporter fold cavity of the Rv1819c is big enough to accommodate about six cobalamin moieties. This indicates that there is no specific, stable binding site for cobalamin in the cavity. This hypothesis is strengthened with the observation that no substrate was eluted during the co-purification experiments of the Rc1819c. However, the presence of several antimicrobial peptides, including Bleomycin, was confirmed in the cavity. Since Mtb is a slow-growing pathogen, such a large cavity in a non-specific exporter could explain the uptake and accumulation of hydrophilic antibiotics inside the bacterial cell (Taber et al. 1987; Aller et al. 2009). In another study, it was observed that Rv1819c helped the Mtb cells in excreting out the antibiotics, serving as a salvage pathway for Mtb (Balganesh et al. 2010). It would be interesting to see if the Rc1819c could rescue the Mtb from antibiotic stress when treated with a specific inhibitor designed using current structural information. If it could do so, specific inhibitors against Rc1819c would prove to be effective antituberculars.

Proteins Involved in Mycobacterial Cell Wall Synthesis and Maintenance

Arabinosyltransferases: Members of Mycobacterial Cell Wall Synthesis Pathway

As described earlier, the unique cell wall of Mtb has a distinctive structure called mycolyl-arabinogalactan-peptidoglycan. It consists of three essential components: mycolic acids, arabinogalactan, and a cross-linking network of peptidoglycans (Alderwick et al. 2015) synthesized by various transferases and synthases unique to mycobacteria. Recently, cryo-EM enabled the structure determination of some of the key enzymes involved in cell wall biosynthesis. These structures hold particular importance in anti-TB drug development since most of the constituents associated with these enzymes are exclusive to Mtb and thus could act as excellent drug targets. One example is membrane-associated arabinosyltransferases EmbA, EmbB, EmbC enzymes that are members of the mycobacterial cell wall synthesis pathway against which the drug ethambutol (EMB) is considered to be active. EMB is a front-line antitubercular used to treat multi-drug resistant TB (MDR-TB) (Sreevatsan et al. 1997). Interestingly, mutations in these arabinosyltransferases result in resistance to EMB (Safi et al. 2008; Sun et al. 2018).

Structures of EmbA-EmbB and EmbC-EmbC complexes in different states, i.e., bound to their glycosyl donor and acceptor, EMB, were determined (Zhang et al. 2020b). These structures help in elucidating mechanisms of EmbA-EmbB and EmbC-EmbC complexes and mode of inhibition by EMB. EmbA and EmbB together form a heterodimer, while EmbC forms a homodimer for its activity. EmbB, a fifteen TMH spanning protein, catalyzes the transfer of arabinose from the donor decaprenyl-phosphate-arabinose (DPA) to its arabinosyl acceptor. On the cytoplasmic face of EmbB is an acyl-carrier protein (AcpM), which is suggested to be associated with the transferase activity. The DPA and di-arabinose bound structures help us understand the overall mechanism of catalysis. The EmbA-EmbB complex catalyzes the branching reaction, while the elongation reaction is catalyzed with the help of the EmbC dimer. In another report, the complex EmbB-EmbB’-AcpM2 in resting-state on binding to DPA gets activated, as shown in Fig. 2a (Zhang et al. 2020a). It leads to the transfer of arabinose from the donor DPA to its arabinosyl acceptor. EMB bound to EmbB structure explains the interaction of the drug with the active site in EmbB (Fig. 2a). The drug EMB competes for the binding sites for substrates in EmbB and EmbC (Goude et al. 2009). The 3.3 Å EM structures of EmbB (substrate and drug bound) provided crucial insights into the mode of action of substrate binding and presented a map of how resistance against ethambutol could have occurred due to mutations accumulated around the active site (Tan et al. 2020a).

Fig. 2.

a Mycobacterial Arabinosyltransferase complex. The complex is composed of two chains, each of EmbB and AcpM. On binding of DPA (red-green spheres), resting-state complex (PDB: 7BX8) is activated (PDB: 7BWR). The arabinosyltransferase is inhibited by ethambutol (Etmb: red) binding in the active site in EmbB (7BVC). b The barrel-shaped MsFAS is a hexamer with one monomer chain shown in cyan (PDB: 6GJC). Each chain is made up of 6 subunits, namely—acetyltransferase (AT), enoyl reductase (ER), dehydratase (DH), malonyl transacylase (MPT), ketoacyl reductase (KR), and ketoacyl synthase (KS) (Color figure online)

Similarly, arabinofuranosyltransferase D (AftD) is another class of transferase. The structure from M. abscessus at 2.9 Å resolution (Tan et al. 2020b) revealed similarities in overall architecture with EmBA, EmbB, and EmbC (Zhang et al. 2020b). The AftD structure is α-helix rich with sixteen TMHs and a cytoplasmic portion consisting of both α and β components. The cytoplasmic α/β folds are homologous to EmbC, three carbohydrate-binding modules (CBMs), and one structural β-sandwich domain. Besides, AftD has a conserved glycosyltransferase (type C) fold, which binds to complex arabinose glycans. The high-resolution structure of AftD enabled the identification of the active site for the transferase activity and highlighted the importance of Arg1389 residue.

Mycobacterial Fatty Acid Synthase

Mycolic acid is a significant and unique fatty acid found in the Mtb cell wall playing a vital role in pathogenicity (Marrakchi et al. 2014). The enzyme system that catalyzes the synthesis of fatty acid precursors of mycolic acids is known as the FAS complex. In Mtb, there are two types of FAS systems FAS1 and FAS2. FAS1 is found in other mycolic acid producers like certain Bifidobacteriales and Actinomycetales species and in Mtb, it is known to produce fatty acid precursors with a carbon chain length of C16-18 and C26. However, in M. smegmatis, FAS produces C24 fatty acids instead of C26 (Trivedi et al. 2004). FAS2 is involved in the elongation of products of FAS1 in Mycobacteria (Takayama et al. 2005). With the help of other enzymes, FAS2 converts C16-18 long products of FAS1 to C45-64 long meroacids, which are further converted to mycolic acids (Bhatt et al. 2007).

The first mycobacterial FAS1 structure was reported at a global resolution of 7.5 Å from M. smegmatis, succeeded by a 3.3 Å structure from Mtb, determined using single-particle cryo-EM (Boehringer et al. 2013; Elad et al. 2018). The FAS1 complex structure appears like a barrel of ~ 25 nm diameter. Even though the resolution is not high, almost all the helices were resolved in the density map. Although separate β-strands were not visible, their presence could be confidently marked due to flattened density clouds corresponding to β-sheets in the MsFAS model. At the same time, these features could be characterized in Mtb FAS1. However, a crucial difference in the reactive pocket of fungal FAS1 and MsFAS is visible. MsFAS at the opening of the reactive pocket is broader than that observed in fungal FAS1 (Gipson et al. 2010). These differences in the cleft size of fungal and mycobacterial FAS1 could enable Mtb FAS1 to produce C26 fatty acids.

The multifunctional, mycobacterial FAS1 is a 2MDa complex consisting of α6 homo-hexamers (Fig. 2b). Each protomer is a product of six subunits named acetyltransferase (AT), enoyl reductase (ER), dehydratase (DH), malonyl transacylase (MPT), ketoacyl reductase (KR), and ketoacyl synthase (KS), assuming respective function as indicated by its name (Fig. 2b). Although considered homologous, M. smegmatis FAS1 (MsFAS) is 900 amino acid residues shorter than the fungal FAS1. This difference could be attributed to the presence of the C-terminal phosphopantetheinyl transferase domain in the fungal FAS. This structural data, particularly regions that are different from fungal FAS, can be used for virtual screening and identification of drug candidates that could target mycolate synthesis.

Electron Transport Chain Proteins are Important Therapeutic Targets

F-type ATP Synthase

The mycobacterial F-type ATP synthase is an essential enzyme among its respiratory chain protein members, which provides ATPs crucial for survival. Encoded by unc operon, the ATP synthase consists of six subunits. F₁ subunit crystal structure had been reported (Zhang et al. 2019a). However, the complete enzyme structure was lacking, which was recently reported from M. smegmatis using cryo-EM (Fig. 3a) (Guo et al. 2020a).

Fig. 3.

The complete F-type ATPase complex. a F₀ is the membrane-bound region that mainly consists of a C-ring. The F₁ is the peripheral region where ATP is synthesized (PDB: 7JG5). b SF₀ regions with and without BDQ (dark red) bound to it. c BDQ binds in two sites. The leading site lies between ‘a’ and ‘c’ subunits, while the lagging site lies only on the ‘c’ subunit (Color figure online)

The structure of mycobacterial F-type ATP synthase holds particular importance since the recently approved antitubercular drug BDQ specifically inhibits mycobacterial F-type ATP synthase (Haagsma et al. 2009). It was speculated that it binds either to the c subunit of the enzyme or targets ε subunit (Preiss et al. 2015; Kundu et al. 2016). However, the recent cryo-EM structure describes the full-length enzyme in different drug bound states while resolving all of its subunits. The EM structure remarkably reveals that there are in all 7 BDQ binding sites at F₀ region (Fig. 3b) in the ATP synthase: 5 BDQ molecules exclusively bind to the c chains of the ring called the ‘lagging site’ (Fig. 3c) while the remaining 2 interact with the subunit a and subunit c, called the ‘leading site’ (Fig. 3c). These findings have ruled out the proposed interaction of the BDQ with the ε subunit and have elucidated the overall mechanism and biochemistry of the drug action (Guo et al. 2020b). A recent report also indicates that the drug BDQ can target human mitochondrial ATPase (Luo et al. 2020). This has posed serious concerns regarding the treatment of Multi/Extremely drug resistant (M/XDR) TB. Thus, the availability of the complete structure of mycobacterial ATPase is a significant advancement in designing highly specific inhibitors.

Mycobacterial Respiratory Supercomplex

Several membrane-bound multi-protein enzyme complexes together form the respiratory chain in Mtb (Gong et al. 2018). Popularly termed as respiratory supercomplexes, which help transfer electrons from reduced nicotinamide adenine dinucleotide (NADH) to molecular oxygen (O₂), thus linking this electron transfer to transmembrane proton translocation (Roy and Wani 2020). The net result is the generation of a proton gradient that drives the ATP production and transport across the membrane (Rao et al. 2008).

The M. smegmatis respiratory supercomplex’s (Fig. 4a1) structure was determined at 3.3–3.5 Å resolutions with its crucial cofactors like heme clearly visible in the electron density map (Fig. 4a2) (Wiseman et al. 2018). The complex is primarily made up of two sub-complexes, complex III and complex IV. The dimer of complex III lies in the middle and is flanked by individual complex IV subunits from both sides. The center for oxygen reduction lies in complex IV, while the quinol site is present in complex III. The electron transfer between these two sub-complexes is facilitated via a cytochrome subunit bridged between complex III and IV. The complex of dimeric C_III–C_IV arrangement is C2 symmetric with dimensions of 200 × 70 × 120 Å. Such symmetry is the first of its kind observed among respiratory supercomplexes so far. At a global resolution of 3.5 Å, all the prosthetic groups of respiratory supercomplex, menaquinone, and heme molecules could be resolved and built. The two menaquinone molecules could be observed in the conserved quinone binding site located in the C_III complex. The complex C_III comprises of QcrA, QcrB, and QcrC subunits, while the complex C_IV consists of CtaC, CtaD, CtaE, and CtaF subunits. When the supercomplex is in an open state, the cc head of the QcrC is bound to only complex C_IV, while in the closed state, the head domain is associated with both C_III and C_IV complexes (Gong et al. 2018).

Fig. 4.

Structure of respiratory supercomplex (PDB: 6HWH). a1 The supercomplex is composed of two subcomplexes and some unidentified peptides (grey). Complex IV (blue) consists of CtaC, CtaD, CtaE, and CtaF units. Complex III is composed of QcrA, QcrB, and QcrC domains. Open QcrC is in orange, while closed conformation is in red. a2 The electron from heme bL is transferred to heme bH rather than to FeS. The cardiolipins (CDL) are anchored to the two Arg residues near the menaquinone binding site in QcrB and the helix of QcrC that embeds in the membrane. The heme cofactors are shown in purple and the cardiolipin in green. b The MtClpP1P2 complex (PDB: 6VGK). The heptamer ClpP1 (cyan) ring is placed below the heptameric ClpP2 (maroon) ring, but each monomer of ClpP1 interacts with its ClpP2 counterpart. c The ClpB is a hexamer of six protomers. From the top view, the core of the free ClpB appears like a tunnel (PDB: 6ED3). On the binding of nucleotides (ADP: blue spheres, ATPγS brown spheres) and the substrate—casein (red), the size of the tunnel shrinks due to the movement of protomers (e.g., P1), and the overall structure becomes more compact with the movement of each monomer subunit (PDB: 6DJU) (Color figure online)

Mycobacterial bc-type C_III supercomplex appears similar to the dimeric association, as seen in bacterial bc₁-type and mitochondrial C_III; however, certain subtle structural differences are present (Xia et al. 1997). Q203, an imidazopyridine amide, is a candidate reported to be an effective inhibitor of cytochrome bc₁-aa₃ complex, binds explicitly to QcrB of the supercomplex (Lee et al. 2020). Since complex C_III is an essential ROS production site, it is a crucial target to produce lethal stress in mycobacteria (Zhao and Drlica 2014). The superoxide dismutase (SodC) enzyme is known to protect the electron transport chain (ETC) of mycobacteria from this ROS stress when phagocytized by human macrophages, thus helping in the survival of the bacterium inside the host lungs (D’Orazio et al. 2001). It has been found that the SodC is integral to the respiratory supercomplex situated at the periplasmic face. It is probably involved in scavenging the ROS produced by the host, providing a robust defense mechanism to Mtb (Bhattacharya 2015). In summary, the cryo-EM structure of a C_III–C_IV respiratory supercomplex from M. smegmatis illustrates how an electron transfer pathway occurs in complex C_III and reaches the final oxygen reduction step in the complex C_IV, a new branch of electron transfer for energy transduction in association with superoxide dismutase domain acting as the detoxing agent of ROS.

Structural Insights into Key Mycobacterial Proteases

ClpP1P2 Protease

Proteostasis is a necessary process for maintaining overall protein turnover in the cell using various synthesis and lysis pathways. Specific proteolytic machines in assistance with AAA + unfoldase (AAA: ATPases Associated with diverse cellular Activities) partner recognize certain substrate proteins and mediate their unfolding and further carry out the proteolytic activity (Sauer and Baker 2011). Among such proteases, the ClpP system (Caseinolytic proteases P) is crucial as it helps maintain homeostasis and assist virulence in several bacteria. Particularly in Mtb, the ClpP1P2 protease system is of major importance and indispensable for bacterial growth and virulence (Frees et al. 2014; Bhandari et al. 2018), making it an attractive drug target. Unlike other bacteria, Mtb contains two genes, clpP1 and clpP2, encoding for MtClpP1 and MtClpP2 proteins, respectively (Personne et al. 2013; Alhuwaider and Dougan 2017).

The structures of MtClpP1P2 were recently solved in two conformations; an apo form, which is a compact conformation, and cyclic acyldepsipeptides (ADEPs) bound conformation, which is relatively more relaxed and ordered at the N-terminus. The overall ClpP complex (single ClpP protein 200 residues long) appears like a barrel of about 83 Å height with a central channel formed by two rings stacked one upon another (Fig. 4b). The products of gene clp1 and clp2, i.e., proteins Clp1 and Clp2, form a heptameric ring. The ClpP2 heptamer ring is stacked above that of the ClpP1 ring coaxially to produce a barrel-like structure. In the bacterial ClpP complex, a ‘handle’ region made up of a helix and a β-sheet in each protomer, mediates the interactions within the rings (Liu et al. 2014). The handle region helps the catalytic triad Asp-His-Ser maintain the active site's geometry for proper binding of the substrate polypeptide (Szyk and Maurizi 2006). The 3.0 Å resolution structure of the apo form of mycobacterial ClpP complex suggests that the β-strands in the handle region are disordered, leading to the distorted catalytic triad. This explains the inactivity of the enzyme system in the apo form. On binding with the ADEP, there is no change in the overall architecture of the 'handle' domain (Vahidi et al. 2020).

According to one report, the chloromethyl ketone derivative of compound Bortezomib specifically inhibits the MtClpP1P2 system, imparting cytotoxic effects on Mtb (Moreira et al. 2017). In the same report, it was shown that the inhibitor does not act on human proteases. This structural information of the MtClpP1P2 system could be exploited to design inhibitors highly specific to the protease active site and could be further developed as novel antitubercular. Candidates like Lassomycin, Rufomycin bind to the ClpC1- an ATP unfoldase, thereby affecting the ATP-dependent protein unfolding from proteolysis, ultimately showing a bactericidal effect on active and latent TB infections (Dougan et al. 2020).

ClpB—an ATP-Driven Disaggregase

Like the ClpP system described earlier, another protease system, known as ClpB disaggregase, functions in association with heat-shock proteins. In bacteria, ClpB is a ring-shaped ATP-driven disaggregase belonging to the family of Hsp100 chaperones (Doyle et al. 2013). Under stress conditions, the ClpB, in association with other chaperons and accessory proteins, helps specific proteins refold from an aggregated state, thus helping the cell survive and overcome the stress (Mogk 1999; Doyle and Wickner 2009; Lupoli et al. 2016). Like Hsp104, ClpB utilizes ATP hydrolysis energy, and thus, it is known as 'protein disaggregase,' where it carries polypeptides through its central pore (Weibezahn et al. 2004). The cryo-EM structure of Mtb ClpB was determined at ~ 3.8–3.9 Å, in different conformations (AMPPNP bound conformer, open and closed state, AMPPNP- Adenylyl imidodiphosphate) (Yu et al. 2018). The structure indicates that ClpB is a hexamer arranged in a ring (Fig. 4c). Each protomer consists of three domains: an N-terminal domain (NTD), and NBD1 and NBD2 as two AAA+ type nucleotide domains that carry out ATP assisted peptide translocation (Gates et al. 2017). Thus, each hexamer accommodates 12 NBDs. Eukaryotic Hsp104 and mycobacterial ClpB belong to the same family (Doyle et al. 2013). Still, there are key differences, especially in the NBD regions of these two proteins. The Mtb ClpB has both NBD1 and NBD2 moving in an upward direction. However, in Hsp104, the two NBDs move in opposite directions, i.e., if NBD1 moves upwards, then the NBD2 orients itself downwards. This movement creates a temporary gap in the Hsp104 ring, which is absent in ClpB. This structural difference could probably reflect a different mode of ATP hydrolysis in ClpB and Hsp104. Further experiments, however, are warranted to confirm this observation. ClpB is crucial for Mtb survival inside the host (Lupoli et al. 2018). The insights gained from the ClpB structure could help in developing it into a novel anti-TB drug target.

Cryo-EM Structures that Elucidate Basic Cellular Processes in Mtb

Apart from the proteins mentioned above, a few other crucial structures were reported recently. These structures are essential considering their druggability but are more significant in terms of bacterial physiology and have provided us with a more in-depth understanding of mycobacteria's underlying cellular processes. The list includes Mtb and M. smegmatis ribosomes, small heat-shock protein Acr1, proteasome assembly and its bacterial proteasome activator (Bpa), nuclease AdnAB motor, RNA polymerase, and few others (Table 1). The structure of α-crystallin related protein 1 is among the first few mycobacterial protein structures determined using cryo-EM (Kennaway et al. 2005).

The cryo-EM structures of ribosomes describe how Mtb remodels its ribosomes in Zinc-depleted conditions (Li et al. 2018a). The 70S structure has underlined the differences between Mtb and other bacterial ribosomes, especially the variations in lengths of specific rRNA helices (Li et al. 2018b). The 70S structure now enables us to understand the movement between specific ribosomal proteins, handle, small subunit, and other regions/domains of the complete ribosome assembly (Yang et al. 2017). These structures offer detailed information about the transcription occurring at the ribosome. Additionally, two non-ribosomal proteins were detected in these structures. These two proteins could be some transcription regulators; however, these are yet to be identified. The EM reconstructions of the M. smegmatis 70S ribosomes in the hibernating state, trans-translating state (Fig. 5a), and the peptidyl tRNA bound state at the resolutions 4.1 Å, 12.5 Å, and 3.4 Å, respectively, highlight the new role of bS1 protein in 70S protection during hibernation in mycobacteria. With these structures' help, we now have a complete snapshot of H54a-bS1 interactions that prevent subunit dissociation and degradation (Mishra et al. 2018).

Fig. 5.

a The overall architecture of tmRNA and SmpB in the 70S bound state—the trans-translation. The SmpB is a small protein (green) that helps in the stabilization of tmRNA at A and P-tRNA binding sites (PDB: 5ZEY). b The open clamp structure of the Mtb RNAP bound to Fidaxomicin (in cyan), which stabilizes the clamp in a fully open position without DNA in the active site cleft (PDB: 6BZO). The Fidaxomicin binds in the narrow gap between the clamp and the RNAP, as shown in the inset. c Overlapping structure of AdnAB helicase-nuclease before (PDB: 6PPR) and after (PDB: 6PPU) cleavage DNA-complex. Pre-cleavage DNA is shown in orange, while post-cleavage is in red. d PafE-doubly capped (PDB: 6BGL), and PafE-singly capped (PDB: 6BGO) 20S core particle in Mtb. The GQYL motif (yellow spheres) can be seen in the doubly capped CP complex. This motif enables PafE to mount on the α ring, thus allowing the substrate to enter (Color figure online)

Since, using cryo-EM, protein structures could be captured in various intermediate steps of transcription, they improve the understanding of the underlying conformational transitions. The available EM structures of mycobacterial RNA polymerase in core and holoenzyme containing σ^A—a principal sigma factor form have filled this gap (Kouba et al. 2019). These structures depict the steps where the promoter partially melts within the RNA polymerase cleft. This leads to the restriction of DNA at the RNA polymerase active site. The structures of RNA polymerase-promoter DNA complex intermediates elaborate on how and why clamp opening is essential to open a passage for the entry of single-stranded DNA into the active pocket, including fork-loop 2 and switch 2 structures in promoter melting (Boyaci et al. 2019). This RNA polymerase is arrested by antibiotic Fidaxomicin, in an open state, i.e., Fidaxomicin on binding in the cleft of RNA polymerase when in an open state (Fig. 5b) halts the transcription by stopping the promoter from interacting with the RNA polymerase (Boyaci et al. 2018; Lin et al. 2018). Alongside transcription regulation, cryo-EM also sheds light on other molecular machines such as those involved in homologous recombination. AdnAB is a helicase-nuclease present in mycobacteria. It is a dimeric complex with a C-terminal nuclease domain that creates cleavage of 5′ strand DNA. The structures of AdnB in the absence of DNA and complex with forked duplex DNAs before and after cleavage of 5′ ssDNA describe the process of DNA double-strand break resection in M. smegmatis (Fig. 5c) (Jia et al. 2019).

Proteasomes are the assemblies of proteins that perform regulated proteolysis at times required by the cell (Becker and Darwin 2017). For example, the mycobacterial proteasome is activated by proteasome accessory factor E (PafE) (Fig. 5d). This activation promotes proteolysis through proteasome, helping in the virulence of Mtb in the human host. PafE binds to proteasome via glycine–glutamine–tyrosine–leucine (GQYL) motif at its C terminus, independent of ATP. This binding stimulates proteolysis (Hu et al. 2018). Like PafE, Bpa is another molecule that activates the 20S proteasome with the GQYL motif's help (Bolten et al. 2016).

S-Adenosylmethionine IV Riboswitch RNA

In bacteria, specific RNAs can regulate downstream gene expression when bound to cellular metabolites, especially in response to a change in those particular metabolites' concentration. Such RNAs are known as riboswitches. Even though riboswitch RNA does not fall into the membrane protein category, its structure holds particular importance. Despite its small size of 40 kDa, a relatively high-resolution EM structure was determined. These metabolite-binding riboswitches are highly specific but non-coding in nature. The metabolite S-adenosylmethionine (SAM), when acting as a ligand for riboswitches, regulates sulfur metabolism in bacteria (Roth and Breaker 2009).

SAM acts as a cofactor in several methylation reactions, wherein it particularly recognizes seven types of riboswitches like SAM-I, SAM-II… to SAM VI, and SAM-I/IV (Mirihana Arachchilage et al. 2018). SAM-I, SAM-I/IV, and SAM-IV are commonly found SAM riboswitches; crystal structures are already available for them except SAM-IV (Montange and Batey 2006; Gilbert et al. 2008; Lu et al. 2008; Trausch et al. 2014; Huang and Lilley 2018). Recently, the SAM-IV riboswitch cryo-EM structures in both apo and SAM-bound forms were successfully determined at an overall resolution of 3.7 Å and 4.1 Å, respectively (Zhang et al. 2019b). SAM-IV riboswitch comprises of P1, P2a, P2b, P3, and P5 as five helices with two 'pseudoknot' (PK) folds, PK-1 and PK-2. The comparison of SAM-IV structure with that of SAM-I marks critical differences between these two structures. The SAM-IV contains a pseudoknot PK2, which is not seen in SAM-I but lacks the P4 helix present in SAM-I. The kink-turn motif in SAM-I and IV contains six and four nucleotides, respectively (Montange and Batey 2006). It can be noticed that the SAM-I/IV riboswitch contains the P4 helix but lacks PK1 pseudoknot. However, the P4 helix is present in the SAM-IV riboswitch. Despite all these significant structural differences among these three classes of riboswitches (SAM-I, SAM-I/IV, and SAM-IV), the overall core topology at the SAM binding site in these riboswitches remains the same.

Additional Cryo-EM Structures that could be Novel Drug Targets

Despite the recent progress in structure determination of Mtb proteins, there are still several proteins that remain to be explored not just for drug discovery purposes but also to delineate the mechanism of action of crucial enzymes involved in different metabolic processes.

Phenolphthiocerol/phthiocerol polyketide synthase subunit E (PpsE), a type I polyketide synthase, is involved in the elongation of C22-24 fatty acids by adding malonyl-CoA and methylmalonyl-CoA extender units. This elongation step yields phthiocerol derivatives (Astarie-Dequeker et al. 2009). In Mtb, PpsE is proven to be associated with the ESX-1 secretion system (Augenstreich et al. 2017), thus makes it an exciting target. The msl3 gene product, mycolipanoate synthase, is a homodimer. It is a part of the polyacylated trehalose synthesis pathway. Mutations in this gene lead to cell aggregation (Dubey et al., 2002).

Another candidate protein, Lnt, is 93 kDa in size and catalyzes the N-acylation of the N-terminal cysteine of apolipoprotein (Tschumi et al. 2009). Specific inhibitors of Lnt could be designed based on the structural information to study the after-effects of tri-acetylation inhibition in Mtb cell morphology. Apart from such membrane proteins, other relatively smaller proteins like iron import ATP-binding protein, Serine/Threonine-protein kinase, Protoheme IX farnesyltransferase should be targeted for structure determination since these hold great potential as novel drug targets (Nalamolu et al. 2019).

Cryo-EM and Vaccine Development

‘Structural vaccinology’ is a rational approach for vaccine development. It is primarily based on determining the atomic structure of the antigen or antigen–antibody complex, mainly against viruses (Anasir and Poh 2019). The cryo-EM technique facilitated the structure determination of giant viruses like the herpes simplex virus for vaccine development. (Dai and Zhou 2018). Based on a similar approach, vaccines could be developed against different viruses. Recent EM structures of the African swine fever virus (ASFV)—one of the most complex DNA viruses could help in a more in-depth understanding of the virus's structure–function relationship (Gallagher and Harris 2020). Such progress should aid vaccine development and could form the basis of a new era of ‘Structural Vaccinology.’ During the recent SARS-CoV-2 pandemic, several structures have been deposited that have proven instrumental in research and development on drug discovery and vaccine development for SARS-CoV-2 (Walsh et al. 2020). Similarly, in TB's case, structural information from the above discussed Mtb proteins could be utilized to develop an effective treatment/vaccine against all TB types towards worldwide TB control by 2030 as per WHO’s goals.

At present, 14 TB vaccines are at different stages of clinical trials, while the live, attenuated Mycobacterium bovis bacille Calmette-Guérin (BCG) vaccine is still the most widely used (Schrager et al. 2020). With the amalgamation of available cryo-EM information and additional experiments to understand mycobacterial membrane using EM and tomography techniques, improved and effective vaccine alternatives to the classical BCG vaccine may be an achievable goal.

Concluding Remarks

As mentioned earlier, membrane protein structure determination is a cumbersome process since membrane proteins are difficult to crystallize. However, in the past decade, cryo-EM technology has taken a giant leap forward, making these limitations almost invisible. Since 2005, about 75 EM structures have been deposited (as updated on July 2020) from mycobacteria in the PDB. We have briefly discussed key membrane proteins that are therapeutically important. These structures include protein candidates from various biological pathways. Some are associated with cell growth and metabolic pathways, while others are associated with virulence, defense, and survival strategies. The snapshots provided by cryo-EM structures depicting proteins in various stages of their activity help us establish underlying mechanisms with structural evidence. Several structures of ribosomes help us visualize different steps in transcription. Not only membrane protein structures, we now have snapshots of membrane organization, which would prove instrumental in the expansion of knowledge of material transport across the mycomembrane, especially when mechanistic insights into the functioning of secretion systems and transporters have started to emerge, thanks to cryo-EM.

In recent years, we have witnessed a tremendous increase in structure determination using cryo-EM. Compared to the past two decades, we see exponential growth in the number of membrane protein structures determined using EM in the past three years (Supplementary Table S1). These membrane proteins are associated with crucial pathways involved in bacterial metabolism and/or virulence; at the same time, they are non-native to human physiology. Hence, biosynthesis or metabolic pathways associated with these proteins could serve as a goldmine of novel and effective anti-TB drug targets.

Supplementary Information

Below is the link to the electronic supplementary material.

Abbreviations

AAA

ATPases associated with diverse cellular activities

ABC

ATP-binding cassette

AcpM

Acyl-carrier protein M, Acr1: alpha-crystallin-related protein 1

Acr1

Alpha-crystallin-related protein 1

ADEP

Acyldepsipeptide

Adn

ATP-dependent nuclease

AftD

Arabinofuranosyltransferase D

AMPPNP

Adenylyl imidodiphosphate

BBH

Benzyloxybenzylidene-hydrazine

BDQ

Bedaquiline

Bpa

Bacterial proteasome activator

CBM

Carbohydrate-binding module

CDL

Cardiolipin

C_III2C_IV2SOD₂

C_III and C_IV subunits of respiratory supercomeplex bound to superoxide dismutase in C2, symmetry

Clp

Caseinolytic proteases

Cryo-EM

Cryo-Electron Microscopy

Cryo-ET

Cryo-Electron Tomography

Cta

Subunits of aa₃-type cytochrome c oxidase

CTD

C-terminal domain

DPA

Decaprenyl-phosphate-arabinose

Ecc

ESC conserved component

EMB

Ethambutol

ESAT-6

6 KDa early secretory antigenic target

Esp

ESX-1 secretion-associated protein

ESX

ESAT-6

ETC

Electron transport chain

FAS

Fatty Acid Synthase

Galf

Galactofuranosyl

GLF-CMK

Z-Gly-Leu-Phe-chloromethyl ketone

GQYL

Glycine–glutamine–tyrosine–leucine

HIV

Human immunodeficiency virus

HSP

Heat shock protein

MPY

Mycobacterial-specific protein Y

MSD

Membrane spanning domain

Mtb

Mycobacterium tuberculosis

M/XDR

Multi/extremely drug resistant

NBD

Nucleotide-binding domain

PafE

Proteasome accessory factor E

PCAT

Peptidase-containing ATP-binding cassette transporters

PDB

Protein data bank

PK

Pseudoknot

PpsE

Phenolphthiocerol/phthiocerol polyketide synthase subunit E

RbpA

RNA polymerase-binding protein A

RNAP

RNA polymerase

ROS

Reactive oxygen species

SAM

S-Adenosylmethionine

SARS-CoV-2

Severe Acute Respiratory Syndrome Coronavirus 2

Sr. No.

Serial Number

TB

Tuberculosis

TMH

Trans-membrane helix/helices

WHO

World Health Organization

Author Contributions

The manuscript was conceptualized, designed, and written by ADB, PJP, and JK.

Funding

This work was funded by a Centre of Excellence Grant BT/PR15450/COE/34/46/2016 from the Department of Biotechnology, India. ADB gratefully acknowledges the financial support from the DBT-RA Program in Biotechnology and Life Sciences (India).

Declarations

Conflict of interest

PJP is co-founder and shareholder of www.cryosol-world.com.