MoonProt 2.0: an expansion and update of the moonlighting proteins database

Chen, Chang; Zabad, Shadi; Liu, Haipeng; Wang, Wangfei; Jeffery, Constance J.

doi:10.1093/nar/gkx1043

Cited by 91 publications

(71 citation statements)

References 17 publications

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“…The paradigm member of NrtR family is believed to possess the Nudix pyrophosphatase enzymatic activity in addition to its DNA-binding ability (10), and thus it can be classified as a moonlighting protein. A moonlighting protein refers to a single protein with dual independent roles that are not due to gene fusion (35). However, the Nudix hydrolysis activity was lacking in the SsNrtR (Fig.…”

Section: Discussionmentioning

confidence: 99%

Functional definition of NrtR, a remnant regulator of NAD ⁺ homeostasis in the zoonotic pathogen Streptococcus suis

et al. 2019

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NAD+ is an enzyme cofactor required for the 3 domains of life. However, little is known about the NAD+ biosynthesis and salvage pathways in the opportunistic pathogen Streptococcus suis. A genome‐wide search allows us to identify the NAD+ salvage pathway encoded by an operon of nadR‐pnuC‐nrtR (from SSU05_1973 to SSU05_1971 on the reverse strand) in the S. suis 05ZYH33 that causes streptococcal toxin shock–like syndrome. The regulator of this pathway is Nudix–related transcriptional regulator (NrtR), a transcription regulator of the Nudix family comprising an N‐terminal Nudix‐like effector domain, and a C‐terminal DNA‐binding winged helix‐turn‐helix–like domain. Intriguingly, the S. suis NrtR naturally contains a single amino acid substitution (K92E) in the catalytic site of its Nudix domain that renders it catalytically inactive but does not influence its ability to bind DNA. Despite its lack of enzymatic activity, DNA‐binding activity of NrtR is antagonized by the effector ADP‐ribose. Furthermore, nrtR knockout in S. suis serotype 2 reduces its capacity to form biofilms and attenuates its virulence in a mouse infection model. Genome mining indicates that nrtR appears in a strain‐specific manner whose occupancy is correlated to bacterial infectivity. Unlike the paradigmatic member of NrtR family having 2 unrelated functions (Nudix hydrolase and DNA binding), S. suis 2 retains a single regulatory role in the modulation of NAD+ salvage. This control of NAD+ homeostasis contributes to S. suis virulence.—Wang, Q., Hassan, B. H., Lou, N., Merritt, J., Feng, Y. Functional definition of NrtR, a remnant regulator of NAD+ homeostasis in the zoonotic pathogen Streptococcus suis. FASEB J. 33, 6055–6068 (2019). http://www.fasebj.org

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Section: Discussionmentioning

confidence: 99%

Functional definition of NrtR, a remnant regulator of NAD ⁺ homeostasis in the zoonotic pathogen Streptococcus suis

et al. 2019

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“…Strikingly, POU2F1 is found in nucleoplasm only (35). Due to this, a BLAST is performed and based on the local similarity two proteins are found in the database having moonlighting property (36). Those proteins along with their human specific activities (function 1 (F1) and function 2 (F2)) are reported in Table 1.…”

Section: Resultsmentioning

confidence: 99%

“…Subsequently, a quality assessment analysis makes it clear that which of the residues have higher propensity to lead a healthy binding. In quality assessment, a dihedral chi1 angle clash has been found at residue number 20 which is directly associated with a sequence space module with 17,28,13,35,9,3,36,21,20 residues. Eventually based on inner coupling strength from sequence space, the inner allosteric effects may carry forward though out all the residues.…”

Section: Discussionmentioning

confidence: 99%

“…Along with that, the structure of POU2F1 has been analysed depending on quality assessment and normal mode based structure network. Comparing the sequence and structure space information, the most significant set of residue viz., 3,9,13,17,20,21,28,35,36 have been identified as structural facet for stable binding. It is observed that targeting these residues can help to prevent the monomeric aggregations.…”

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confidence: 99%

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Studying POU2F1 to Unveil the Structural Facet for Pan-Cancer Analysis Considering the Functional Annotations and Sequence-Structure Space Paradigm

Dey

Sen

Maulik

2019

Preprint

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POU domain class 2 homebox 1 (POU2F1) is largely known for its transcription factor(TF) activity. Due to its association with different types of malignancies, POU2F1 becomes one of the key factors in pan-cancer analysis. However, in spite of understanding it as a potential drug target, none of the drug has been designed till date due to its extreme dynamicity. In this article, we have proposed a three fold comprehensive framework for understanding the structural conservation and co-variation of POU2F1. Firstly, a gene regulatory network based non-pathogenic and pathogenic study have been performed to understand the strong association between cancers and POU2F1. After that, based on evolutionary sequence space study, the comparative sequential dynamicity of the protein members of POU domain family has been observed mostly between non-human and human samples. Subsequently, the reciprocity effect of the residual co-variation has been identified through direct coupling analysis. Along with that, the structure of POU2F1 has been analysed depending on quality assessment and normal mode based structure network. Comparing the sequence and structure space information, the most significant set of residue viz., 3,9,13,17,20,21,28,35,36 have been identified as structural facet for stable binding. It is observed that targeting these residues can help to prevent the monomeric aggregations. This study demonstrates-the observed malleability of POU2F1 is one of the prime reason behind its functional multiplicity in terms of protein moonlighting. SIGNIFICANCE POU2F1 is one of the important TFs associated with several malignancies. In spite of orderly stable structure in primitive family proteins, this protein is highly unstable at the monomeric stage. Previous studies show that POU2F1 has a clear association with 121 different diseases. Therefore, it becomes one of the important links in the pan-cancer study. Interestingly, TFs can be considered as a potential drug target. However, it is hardly possible to control the extreme dynamicity of TFs. In this regard, protein moonlighting plays an important role. We have tried to provide a theoretical frame to build understanding on POU2F1. The study provides pathogenic and non-pathogenic connections of the protein in terms of comprehensive and precise Gene Regulatory Network. Subsequently, the instability has been unveiled and the structural facet has been identified. Finally, the specified set of function for a suitable session to target the protein is analyzed based on protein moonlighting properties.

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“…As pointed out by some of us, establishing a causal link between gene essentiality and the biological function of its protein product under scrutiny should be an indispensable step in target validation for drug development [24]. This view is reinforced by the growing number of proteins found to exhibit multiple and unrelated tasks, the so-called moonlighting proteins [38].…”

Section: Discussionmentioning

confidence: 99%

EvaluatingaroAgene essentiality and EPSP synthase vulnerability inMycobacterium smegmatisunder different nutritional conditions

et al. 2020

Preprint

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26The epidemiological importance of bacteria from the genus Mycobacterium is 27 indisputable and the necessity to find new molecules that can inhibit their growth 28 is urgent. The shikimate pathway, required for the synthesis of important 29 metabolites in bacteria, represents a target for inhibitors of Mycobacterium 30 tuberculosis growth. The aroA-encoded 5-enolpyruvylshikimate-3-phosphate 31 synthase (EPSPS) enzyme catalyzes the sixth step of the shikimate pathway. In 32 this study, we combined gene knockout, gene knockdown and kinetic assays to 33 evaluate aroA gene essentiality and the vulnerability of its protein product, 34 EPSPS synthase from Mycobacterium smegmatis (MsEPSPS), under different 35 nutritional conditions. We demonstrate by an allelic exchange-based gene 36 knockout approach the essentiality of MsEPSPS under rich and poor nutritional 37 conditions. By performing gene complementation experiments with wild-type 38 (WT) and point mutant versions of aroA gene, together with kinetic assays using 39 WT and mutant recombinant proteins, we show that aroA gene essentiality 40 depends on MsEPSPS activity. To evaluate MsEPSPS vulnerability, we 41 performed gene knockdown experiments using the Clustered Regularly 42 Interspaced Short Palindromic Repeats interference (CRISPRi) system. The 43 experiments were performed in both rich and defined (poor) media, using three 44 different repression forces for aroA gene. We only observed growth impairment 45 when bacteria were grown in defined medium without supplementation of 46 aromatic amino acids, thereby indicating that MsEPSPS vulnerability depends on 47 catalyzes the sixth step of the shikimate pathway, the aroA-encoded 5-51 enolpyruvylshikimate-3-phosphate synthase from Mycobacterium smegmatis 52 (MsEPSPS). Combining gene knockout experiments and kinetic assays, we 53 established a causal link between aroA gene essentiality and the biological 54 function of EPSPS protein, which we advocate is an indispensable step for target 55 validation. Moreover, we characterized MsEPSPS vulnerability under different 56 nutritional conditions and found it is a vulnerable target only when M. smegmatis 57 is grown under poor nutritional conditions without supplementation with aromatic 58 amino acids. Based on our findings, we suggest that gene essentiality information 59 should be obtained from gene knockout experiments and not knockdown 60 approaches, as even low levels of a protein after gene silencing can lead to a 61 different growth phenotype when compared to that under its complete absence, 62 as was the case with aroA and MsEPSPS in our study. 63 64 Keywords 65 Gene silencing, Chorismate, Essentiality, Vulnerability, CRISPRi, Molecular 66 genetics. 67 68 69Human tuberculosis (TB) is an important infectious disease that continues 71 to be a public health threat worldwide. Despite the joint global efforts to lower TB 72 burden, which resulted in a 6.3% and 11% cumulative decline in incidence and 73 mortality, respectively, between 2015 and 2018, the End TB...

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MoonProt 2.0: an expansion and update of the moonlighting proteins database

Cited by 91 publications

References 17 publications

Functional definition of NrtR, a remnant regulator of NAD ⁺ homeostasis in the zoonotic pathogen Streptococcus suis

Functional definition of NrtR, a remnant regulator of NAD ⁺ homeostasis in the zoonotic pathogen Streptococcus suis

Studying POU2F1 to Unveil the Structural Facet for Pan-Cancer Analysis Considering the Functional Annotations and Sequence-Structure Space Paradigm

EvaluatingaroAgene essentiality and EPSP synthase vulnerability inMycobacterium smegmatisunder different nutritional conditions

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MoonProt 2.0: an expansion and update of the moonlighting proteins database

Cited by 91 publications

References 17 publications

Functional definition of NrtR, a remnant regulator of NAD + homeostasis in the zoonotic pathogen Streptococcus suis

Functional definition of NrtR, a remnant regulator of NAD + homeostasis in the zoonotic pathogen Streptococcus suis

Studying POU2F1 to Unveil the Structural Facet for Pan-Cancer Analysis Considering the Functional Annotations and Sequence-Structure Space Paradigm

EvaluatingaroAgene essentiality and EPSP synthase vulnerability inMycobacterium smegmatisunder different nutritional conditions

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Functional definition of NrtR, a remnant regulator of NAD ⁺ homeostasis in the zoonotic pathogen Streptococcus suis

Functional definition of NrtR, a remnant regulator of NAD ⁺ homeostasis in the zoonotic pathogen Streptococcus suis