Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase

Kouba, T.; Kovaĺ, T.; Sudzinová, Petra; Pospíšil, Jiří; Brezovská, Barbora; Hnilicová, Jarmila; Šanderová, Hana; Janoušková, Martina; Šiková, Michaela; Halada, Petr; Sýkora, Michal; Barvı́k, Ivan; Nováček, Jiří; Trundová, Mária; Dušková, Jarmila; Skálová, Tereza; Chon, Uree; Murakami, Katsuhiko; Dohnálek, Jan; Krásný, Libor

doi:10.1038/s41467-020-20158-4

Cited by 25 publications

(42 citation statements)

References 66 publications

(72 reference statements)

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“…Studies on HelD from low G+C (Bacillus subtilis) and high G+C (Mycobacterium smegmatis) Grampositives revealed that there are two distinct classes of enzyme, confirmed by phylogenetic and structural analyses (Kouba et al, 2020, Newing et al, 2020, Pei et al, 2020. Class I HelD was described from B. subtilis, whilst the structurally distinct Class II enzyme was identified in M. smegmatis (Kouba et al, 2020, Newing et al, 2020, Pei et al, 2020. Class I and II HelDs have similar motor domains but differ in the structure of their arms and the mechanism by which these arms perform the mechanical activity of removing nucleic acids and recycling RNAP (Kouba et al, 2020, Newing et al, 2020, Pei et al, 2020.…”

Section: Introductionmentioning

confidence: 78%

“…The RNAP trigger loop contains a large insertion in the Deltaproteobacteria (β'In6, Figure 5B) similar to that seen in Gammaproteobacteria, and it was assumed this (and the βIn4 insertion, Figure 5B) would sterically interfere with HelD binding to RNAP in Gram-negative bacteria. Although the trigger loop in the modelled M. xanthus RNAP-HelD complex does clash with HelDMX (Figure 5E and F), this is not extensive and given the inherent flexibility in this domain, small conformational changes would readily enable binding as seen in Gram-positive bacteria (Kouba et al, 2020, Newing et al, 2020, Pei et al, 2020. The CA of HelDMX is similar in size to that of HelDMS (although it does not contain a PCh domain; Figure 5B).…”

Section: A Novel Held Class In Gram-negative Bacteriamentioning

confidence: 97%

“…The recent structures of HelD from B. subtilis and M. smegmatis bound to core RNAP (α2ββ'ω) (Kouba et al, 2020, Newing et al, 2020 are shown in Figure 2A and B, along with the Class I B. subtilis (Figure 2C) and Class II M. smegmatis (Figure 2D) enzymes. HelD has an unusual mode of action dependent on two arms (CA and SCA, Figure 2C and D) attached to the central UvrD-like ATPase motor domain (Head and Torso, Figure 2C and D), in which nucleic acids are pushed out of the active site whilst the DNA binding clamp and RNA exit channels are simultaneously opened, leading to the release of the stalled RNAP (Newing et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…This recycling activity is powered by ATP hydrolysis and the mechanical action of the two arms that flank the motor domain. In the Class I HelD, the long SCA (Figure 2A and C) is able to physically remove nucleic acids from the active site (dotted circle in Figure 2A), whereas in the Class II HelD the SCA is too short, and instead nucleic acid removal is performed by a CA insert called the PCh-loop (Figure 2B and D) (Kouba et al, 2020, Newing et al, 2020. Recent reports also suggest that some Class II HelDs (from M. abscessus and Streptomyces venezuelae) are able to confer rifampicin resistance through removal of rifampicin by the PCh-loop (Hurst-Hess et al, 2021, Surette et al, 2021.…”

Section: Introductionmentioning

confidence: 99%

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Multiple classes and isoforms of the RNA polymerase recycling motor protein HelD

Larsen

Miller

Oakley

et al. 2021

Preprint

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SUMMARYEfficient control of transcription is essential in all organisms. In bacteria, where DNA replication and transcription occur simultaneously, the replication machinery is at risk of colliding with highly abundant transcription complexes. This can be exacerbated by the fact that transcription complexes pause frequently. When pauses are long-lasting, the stalled complexes must be removed to prevent collisions with either another transcription complex or the replication machinery. HelD is a protein that represents a new class of ATP-dependent motor protein distantly related to helicases. It was first identified in the model Gram-positive bacterium Bacillus subtilis and is involved in removing and recycling stalled transcription complexes. To date, two classes of HelD have been identified: one in the low G+C and the other in the high G+C Gram-positive bacteria. In this work we have undertaken the first comprehensive investigation of the phylogenetic diversity of HelD proteins. We show that genes in certain bacterial classes have been inherited by horizontal gene transfer, many organisms contain multiple expressed isoforms of HelD, some of which are associated with antibiotic resistance, and that there is a third class of HelD protein found in Gram-negative bacteria. Therefore, HelD proteins represent an important new class of transcription factor associated with genome maintenance and antibiotic resistance that are conserved across the Eubacterial kingdom.

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Section: Introductionmentioning

confidence: 78%

Section: A Novel Held Class In Gram-negative Bacteriamentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Multiple classes and isoforms of the RNA polymerase recycling motor protein HelD

Larsen

Miller

Oakley

et al. 2021

Preprint

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“…In support of this mechanism, Kouba et al . show that HelRMs can form a complex with RNAP with both σ A and RpbA bound, facilitating transcription initiation following removal of rifamycins (Kouba et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

HelR is a helicase-like protein that protects RNA polymerase from rifamycin antibiotics

Surette

Waglechner

Koteva

et al. 2021

Preprint

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Rifamycin antibiotics such as rifampin are widely used for the management of tuberculosis and other bacterial infections. These drugs inhibit prokaryotic RNA polymerase (RNAP) by preventing elongation of mRNA resulting in cell death. Rifamycin resistance in the clinic is manifested primarily through amino acid substitutions in RNAP that decrease target affinity for the antibiotics. In contrast, environmental bacteria possess a wide variety of highly specific rifamycin enzyme-mediated resistance mechanisms that modify and inactivate the antibiotics by glycosylation, phosphorylation, ADP-ribosylation, or hydroxylation. Expression of rifamycin resistance is controlled by a common 19bp cis-acting rifamycin associated element (RAE) upstream of inactivating genes. Guided by the presence of RAE sequences, we identify an unprecedented ATP-dependent mechanism of rifamycin resistance that acts not by antibiotic inactivation but by protecting the RNAP target. We show that Streptomyces venezuelae encodes a helicase-like protein, HelR, which confers broad spectrum rifamycin resistance. Furthermore, HelR is essential for promoting rifamycin tolerance at inhibitory concentrations, enabling bacterial evasion of the toxic properties of these antibiotics. HelR forms a complex with RNAP in vivo and rescues transcription inhibition by rifampin in vitro. We synthesized a rifamycin photoprobe and demonstrated that HelR directly displaces rifamycins from RNAP. HelR-encoding genes associated with RAEs are broadly distributed in actinobacteria, including many opportunistic Mycobacterial pathogens, which cannot currently be treated with rifamycins. This first report of an RNAP protection protein conferring antibiotic resistance and offers guidance for developing new rifamycin antibiotics that can avoid this mechanism.

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Toward the Burgeoning Optical Sensors with Ultra‐Precision Hierarchical Structures Inspired by Butterflies

Han

Liu

Chi

et al. 2021

Adv Materials Inter

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In recent years, there has been an increasing interest in the novel bioinspired sensors, especially for their selectivity, response time, and sensitivity. Particular attention is paid to the novel optical functional materials that are crucial for the sensors to achieve various energy transduction. Ideally, many critical parameters of the optical sensing materials can be appropriately tailored to meet various specific requirements using optimal design. Over a long and cruel evolution, nature's creatures have created a variety of photonic structures. One impressive example is the iridescent wings of butterfly. The natural photonic crystals on its surfaces have inspired diverse novel designs of optical functional sensing materials, especially in the past three years. Herein, this review mainly discusses recent advances of the burgeoning butterfly‐inspired sensing materials with optical properties that can be modulated in response to different external stimuli. First, their optical sensing performance to infrared radiation/thermal, vapor, liquid, pH, and so on are discussed in details. Then, the fabrication methods and their working mechanisms are also introduced. Furthermore, the general strategies of these emerging sensing materials and their potential applications are also discussed in‐depth as well as their limitations and the future challenges.

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Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase

Cited by 25 publications

References 66 publications

Multiple classes and isoforms of the RNA polymerase recycling motor protein HelD

Multiple classes and isoforms of the RNA polymerase recycling motor protein HelD

HelR is a helicase-like protein that protects RNA polymerase from rifamycin antibiotics

Toward the Burgeoning Optical Sensors with Ultra‐Precision Hierarchical Structures Inspired by Butterflies

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