Rv1416 (ribH)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: 67-dimethyl-8-ribityllumazine synthase
- REFSEQ: 67-dimethyl-8-ribityllumazine synthase
- PATRIC: 67-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)
- TUBERCULIST: Probable riboflavin synthase beta chain RibH (67-dimethyl-8-ribityllumazine synthase) (DMRL synthase) (lumazine synthase)
- NCBI: Probable riboflavin synthase beta chain RibH (6,7-dimethyl-8-ribityllumazine synthase) (DMRL synthase) (lumazine synthase)
- updated information (H37Rv4):
  - gene name: ribH
  - function:
  - reference:
Type: Not Target
Start: 1591671
End: 1592153
Operon:

Trans-membrane region:
Role: I.G.9 - Riboflavin
GO terms:
- GO:0040007 - growth (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0009349 - riboflavin synthase complex (Uniprot)
- GO:0009231 - riboflavin biosynthetic process (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0000906 - 6,7-dimethyl-8-ribityllumazine synthase activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- A6RP[c] + DB4P[c] -> PI[c] + D8RL[c]
Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
Orthologs among selected mycobacteria
Protein structure: 2vi5, 2c9b, 2c9d, 1w19, 1w29, 2c92, 2c94, 2c97, 2vi5
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
2VI5	99%	MYCOBACTERIUM TUBERCULOSIS	LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO N-6-(ribitylamino)pyrimidine-2,4(1H,3H)-dione-5-yl-propionamide
2C9D	99%	MYCOBACTERIUM TUBERCULOSIS	Lumazine Synthase from Mycobacterium tuberculosis Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)HEXANE 1-PHOSPHATE
2C9B	99%	MYCOBACTERIUM TUBERCULOSIS	Lumazine Synthase from Mycobacterium tuberculosus Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)
2C97	99%	MYCOBACTERIUM TUBERCULOSIS	LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 4-(6- chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)butyl phosphate
2C94	99%	MYCOBACTERIUM TUBERCULOSIS	LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) 1,1 difluoropentane-1- PHOSPHATE
2C92	99%	MYCOBACTERIUM TUBERCULOSIS	LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) PENTANE 1 PHOSPHATE
1W29	99%	MYCOBACTERIUM TUBERCULOSIS	Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 1-phosphate
1W19	99%	MYCOBACTERIUM TUBERCULOSIS	Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)propane 1-phosphate
4J07	78%	Mycobacterium leprae	Crystal structure of a PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae
5MPP	46%	Aquifex aeolicus	Structure of AaLS-wt

Links to additional information on ribH:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -6.44 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VKGGAGVPDLPSLDASGVRLAIVASSWHGKICDALLDGARKVAAGCGLDDPTVVRVLGAIEIPVVAQELARNHDAVVALGVVIRGQTPHFDYVCDAVTQG
LTRVSLDSSTPIANGVLTTNTEEQALDRAGLPTSAEDKGAQATVAALATALTLRELRAHS

(Nucleotide sequence available on KEGG)

Additional Information

Analysis of Positive Selection in Clinical Isolates new

Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
- Moldova: 2,057 clinical isolates
- global set: 5,195 clinical isolates from 15 other countries
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	0.81 (0.09)	1.5 (0.34)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link

* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across ~100 conditions

Rv1416/ribH, gene len: 482 bp, num TA sites: 4

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	essential	7H9	HMM	fully saturated, 14 TnSeq libraries combined
in-vitro	Sassetti 2003 Mol Micro	essential	7H9	TRASH	essential if hybridization ratio<0.2
in-vivo (mice)	Sassetti 2003 PNAS	non-essential	BL6 mice	TRASH	essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol)	Griffin 2011 PPath	essential	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	too short	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=0.0)	cholesterol vs glycerol	resampling-SR	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro	Smith 2022 eLife	essential	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	essential	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=0.0)	in-vivo vs in-vitro	ZINB	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal)	Minato 2019 mSys	essential	minimal medium	HMM
in-vitro (YM rich medium)	Minato 2019 mSys	non-essential	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, cofactors)
differentially essential in YM rich medium	Minato 2019 mSys	NO (LFC=2.27)	YM rich vs minimal medium	resampling

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

RNA processing and modification

Energy production and conversion

Chromatin structure and dynamics

Amino acid transport and metabolism

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Nucleotide transport and metabolism

Lipid transport and metabolism

Coenzyme transport and metabolism

Transcription

Translation, ribosomal structure and biogenesis

Cell wall/membrane/envelope biogenesis

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Cell motility

Secondary metabolites biosynthesis, transport and catabolism

Inorganic ion transport and metabolism

Function unknown

General function prediction only

Intracellular trafficking, secretion, and vesicular transport

Signal transduction mechanisms

Extracellular structures

Defense mechanisms

Nuclear structure

Cytoskeleton

BioCyc Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)

Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

BioCyc Transcription factor binding based on ChIP-Seq (Systems Biology)

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings from other targets were found.

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings to other targets were found.

Interactions based on TFOE data (Rustad et al. 2014)

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Not upregulated by other genes.
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Citation	Identification of two proteins that interact with the Erp virulence factor from Mycobacterium tuberculosis by using the bacterial two-hybrid system. LI. Klepp, M. Soria et al. BMC Mol. Biol. 2009	shahanup86	IPI	19159459	Yeast two-hybrid (Physical interaction)
Interaction	PhysicalInteraction Rv1417	shahanup86	IPI		Yeast two-hybrid (Physical interaction) LI. Klepp, M. Soria et al. Identification of two proteins that interact with the Erp virulence factor from Mycobacterium tuberculosis by using the bacterial two-hybrid system. BMC Mol. Biol. 2009
Interaction	RegulatedBy Rv1963c	yamir.moreno	IEP		Proteomic studies. Regulated gene product concentrations measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) using proteomics techniques. MP. Santangelo, FC. Blanco et al. Study of the role of Mce3R on the transcription of mce genes of Mycobacterium tuberculosis. BMC Microbiol. 2008
Citation	Design, synthesis, and evaluation of 9-D-ribitylamino-1,3,7,9-tetrahydro-2,6,8-purinetriones bearing alkyl phosphate and alpha,alpha-difluorophosphonate substituents as inhibitors of tiboflavin synthase and lumazine synthase. authors,M. Cushman,T. Sambaiah,G. Jin,B. Illarionov,M. Fischer,A. Bacher J. Org. Chem. 2004	jjmcfadden		14750781	Inferred from direct assay
Term	EC:2.5.1.9 Riboflavin synthase. - NR	jjmcfadden	NR		Inferred from direct assay authors,M. Cushman,T. Sambaiah,G. Jin,B. Illarionov,M. Fischer,A. Bacher Design, synthesis, and evaluation of 9-D-ribitylamino-1,3,7,9-tetrahydro-2,6,8-purinetriones bearing alkyl phosphate and alpha,alpha-difluorophosphonate substituents as inhibitors of tiboflavin synthase and lumazine synthase. J. Org. Chem. 2004

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