Regulation of the isophthalate catabolic operon controlled by IphR in Comamonas sp. strain E6

Kamimura, Naofumi; Inakazu, Keisuke; Kasai, Daisuke; Fukuda, Masao; Masai, Eiji

doi:10.1111/j.1574-6968.2012.02521.x

Cited by 12 publications

(6 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Many ITTRs that have been reported as activators are thought to bind to the upstream region of the −35 sequence on the target promoter, thus recruiting RNA polymerase (RNAP) (34,35). In contrast, the binding sequences of the repressors HmgR and IphR are located downstream of the −10 sequence on the target promoter (36,37). EMSAs show DesX binding to IR-DA, an inverted repeat sequence that overlaps the −10 sequence of the SLG_25010 promoter (Fig.…”

Section: Discussionmentioning

confidence: 99%

Sphingobiumsp. SYK-6 syringateO-demethylase gene is regulated by DesX, unlike other vanillate and syringate catabolic genes regulated by DesR

Araki

Tanatani²,

Kamimura³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Syringate and vanillate are the major metabolites of lignin biodegradation. In Sphingobium sp. strain SYK-6, syringate is O demethylated to gallate by consecutive reactions catalyzed by DesA and LigM, and vanillate is O demethylated to protocatechuate by a reaction catalyzed by LigM. The gallate ring is cleaved by DesB, and protocatechuate is catabolized via the protocatechuate 4,5-cleavage pathway. The transcriptions of desA, ligM, and desB are induced by syringate and vanillate, while that of ligM and desB are negatively regulated by the MarR-type transcriptional regulator DesR, which is not involved in desA regulation. Here we clarified the regulatory system for desA transcription by analyzing the IclR-type transcriptional regulator desX, located downstream of desA. Quantitative reverse transcription (RT)-PCR analyses of a desX mutant indicates that the transcription of desA was negatively regulated by DesX. In contrast, DesX was not involved in the regulation of ligM and desB. The ferulate catabolic genes (ferBA) under the control of a MarR-type transcriptional regulator FerC are located upstream of desA. RT-PCR analyses suggest that the ferB-ferA-SLG_25010-desA gene cluster consists of the ferBA operon and the SLG_25010-desA operon. Promoter assays reveal that a syringate- and vanillate-inducible promoter is located upstream of SLG_25010. Purified DesX bound to this promoter region, which overlaps with an 18-bp-inverted repeat sequence that appears to be essential for the DNA binding of DesX. Syringate and vanillate inhibited the DNA binding of DesX, indicating that these compounds are effector molecules of DesX.IMPORTANCESyringate is a major degradation product in the microbial and chemical degradation of syringyl lignin. Along with other low-molecular-weight aromatic compounds, syringate is produced by chemical lignin depolymerization. Converting this mixture into value-added chemicals using bacterial metabolism (i.e., biological funneling) is a promising option for lignin valorization. To construct an efficient microbial lignin conversion system, it is necessary to identify and characterize the genes involved in the uptake and catabolism of lignin-derived aromatic compounds and elucidate their transcriptional regulation. In this study, we found that the transcription of desA, encoding syringate O-demethylase in SYK-6, is regulated by an IclR-type of transcriptional regulator, DesX. The findings of this study, combined with our previous results on desR (a MarR transcriptional regulator that controls the transcription of ligM and desB), provide an overall picture of the transcriptional regulatory systems for syringate and vanillate catabolism in SYK-6.

show abstract

Section: Discussionmentioning

confidence: 99%

Sphingobiumsp. SYK-6 syringateO-demethylase gene is regulated by DesX, unlike other vanillate and syringate catabolic genes regulated by DesR

Araki

Tanatani²,

Kamimura³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…The purity of the enzyme preparation was examined by sodium dodecyl sulfate‐12% polyacrylamide gel electrophoresis (SDS‐PAGE). In vitro cross‐linking of ht‐FerC was performed as descried in a previous study (Kamimura et al ., ).…”

Section: Methodsmentioning

confidence: 97%

Characterization of FerC, a MarR-type transcriptional regulator, involved in transcriptional regulation of the ferulate catabolic operon in Sphingobium sp. strain SYK-6

Kasai

Kamimura

Tani

et al. 2012

FEMS Microbiol Lett

Self Cite

View full text Add to dashboard Cite

Sphingobium sp. strain SYK-6 is able to degrade various lignin-derived aromatic compounds including ferulate, vanillate, and syringate. In the SYK-6 cells, ferulate is converted to vanillin and acetyl-coenzyme A (acetyl-CoA) through the reactions catalyzed by feruloyl-CoA synthetase and feruloyl-CoA hydratase/lyase encoded by ferA and ferB, respectively. Here, we characterized the transcriptional regulation of ferBA controlled by a MarR-type transcriptional regulator, FerC. The ferC gene is located upstream of ferB. Reverse transcription (RT)-PCR analysis suggested that the ferBA genes form an operon. Quantitative RT-PCR analyses of SYK-6 and its mutant cells revealed that the transcription of the ferBA operon is negatively regulated by FerC, and feruloyl-CoA was identified as an inducer. The transcription start site of ferB was mapped at 30 nucleotides upstream from the ferB initiation codon. Purified His-tagged FerC bound to the ferC-ferB intergenic region. This region contains an inverted repeat sequence, which overlaps with a part of the -10 sequence and the transcriptional start site of ferB. The binding of FerC to the operator sequence was inhibited by the addition of feruloyl-CoA, indicating that FerC interacts with feruloyl-CoA as an effector molecule. Furthermore, hydroxycinnamoyl-CoAs, including p-coumaroyl-CoA, caffeoyl-CoA, and sinapoyl-CoA also acted as effector.

show abstract

“…strain E6, isolated in Niigata, Japan, is a betaproteobacterial strain capable of degrading phthalate isomers, o -phthalate, terephthalate, and isophthalate ( 1 ), through the protocatechuate 4,5-cleavage (PCA45) pathway ( 2 ). In this strain, the functions and transcriptional regulations of tph , iph , and pmd genes responsible for the catabolism of terephthalate, isophthalate, and protocatechuate (PCA), respectively, have been characterized ( 1 , 3 – 7 ). In addition, a novel tripartite aromatic acid transporter (TAAT) involved in the uptake of terephthalate and isophthalate was discovered ( 8 ).…”

Section: Genome Announcementmentioning

confidence: 99%

Draft Genome Sequence of Comamonas sp. Strain E6 (NBRC 107749), a Degrader of Phthalate Isomers through the Protocatechuate 4,5-Cleavage Pathway

et al. 2015

Self Cite

View full text Add to dashboard Cite

show abstract

Regulation of the isophthalate catabolic operon controlled by IphR in Comamonas sp. strain E6

Cited by 12 publications

References 24 publications

Sphingobiumsp. SYK-6 syringateO-demethylase gene is regulated by DesX, unlike other vanillate and syringate catabolic genes regulated by DesR

Sphingobiumsp. SYK-6 syringateO-demethylase gene is regulated by DesX, unlike other vanillate and syringate catabolic genes regulated by DesR

Characterization of FerC, a MarR-type transcriptional regulator, involved in transcriptional regulation of the ferulate catabolic operon in Sphingobium sp. strain SYK-6

Draft Genome Sequence of Comamonas sp. Strain E6 (NBRC 107749), a Degrader of Phthalate Isomers through the Protocatechuate 4,5-Cleavage Pathway

Contact Info

Product

Resources

About