ArticlePDF Available

The MocR family transcriptional regulator DnfR has multiple binding sites and regulates Dirammox gene transcription in Alcaligenes faecalis JQ135

Authors:
  • shanghai institute of ceramics

Abstract

Microbial ammonia oxidation is vital to the nitrogen cycle. A biological process, called Dirammox (direct ammonia oxidation, NH3→NH2OH→N2), has been recently identified in Alcaligenes ammonioxydans and A. faecalis. However, its transcriptional regulatory mechanism has not yet been fully elucidated. The present study characterized a new MocR‐like transcription factor DnfR that is involved in the Dirammox process in A. faecalis strain JQ135. The entire dnf cluster was composed of ten genes and transcribed as five transcriptional units, i.e., dnfIH, dnfR, dnfG, dnfABCDE and dnfF. DnfR activates the transcription of dnfIH, dnfG, and dnfABCDE genes, and represses its own transcription. The intact 1,506‐bp dnfR gene was required for activation of Dirammox. Electrophoretic mobility shift assays and DNase I footprinting analyses showed that DnfR has one binding site in the dnfH‐dnfR intergenic region and two binding sites in the dnfG‐dnfA intergenic region. Three binding sites of DnfR shared a 6‐bp repeated conserved sequence 5’‐GGTCTG‐N17‐GGTCTG‐3’ which was essential for the transcription of downstream target genes. Cysteine and glutamate act as possible effectors of DnfR to activate the transcription of transcriptional units of dnfG and dnfABCDE, respectively. This study provided new insights in the transcriptional regulation mechanism of Dirammox by DnfR in A. faecalis JQ135. This article is protected by copyright. All rights reserved.
RESEARCH ARTICLE
The MocR family transcriptional regulator DnfR has
multiple binding sites and regulates Dirammox gene
transcription in Alcaligenes faecalis JQ135
Si-Qiong Xu
1
| Xiao Wang
1
|LuXu
1
| Ke-Xin Wang
1
| Yin-Hu Jiang
1
|
Fu-Yin Zhang
1
| Qing Hong
1
| Jian He
1
| Shuang-Jiang Liu
2,3
|
Ji-Guo Qiu
1
1
Key Laboratory of Agricultural and
Environmental Microbiology, Ministry of
Agriculture and Rural Affairs, College of Life
Sciences, Nanjing Agricultural University,
Nanjing, China
2
State Key Laboratory of Microbial Resources,
and Environmental Microbiology Research
Center at Institute of Microbiology, Chinese
Academy of Sciences, Beijing, China
3
State Key Laboratory of Microbial
Technology, Shandong University, Qingdao,
China
Correspondence
Ji-Guo Qiu, Key Laboratory of Agricultural and
Environmental Microbiology, Ministry of
Agriculture and Rural Affairs, College of Life
Sciences, Nanjing Agricultural University,
Nanjing, China.
Email: qiujiguo@njau.edu.cn
Funding information
National Key R&D Program of China,
Grant/Award Number: 2019YFA0905500;
National Natural Science Foundation of China,
Grant/Award Numbers: 32070092, 32170128
Abstract
Microbial ammonia oxidation is vital to the nitrogen cycle. A biological pro-
cess, called Dirammox (direct ammonia oxidation, NH
3
!NH
2
OH!N
2
), has
been recently identified in Alcaligenes ammonioxydans and Alcaligenes fae-
calis. However, its transcriptional regulatory mechanism has not yet been
fully elucidated. The present study characterized a new MocR-like transcrip-
tion factor DnfR that is involved in the Dirammox process in A. faecalis
strain JQ135. The entire dnf cluster was composed of 10 genes and tran-
scribed as five transcriptional units, that is, dnfIH,dnfR,dnfG,dnfABCDE
and dnfF. DnfR activates the transcription of dnfIH,dnfG and dnfABCDE
genes, and represses its own transcription. The intact 1506-bp dnfR gene
was required for activation of Dirammox. Electrophoretic mobility shift
assays and DNase I footprinting analyses showed that DnfR has one bind-
ing site in the dnfH-dnfR intergenic region and two binding sites in the dnfG-
dnfA intergenic region. Three binding sites of DnfR shared a 6-bp repeated
conserved sequence 50-GGTCTG-N
17
-GGTCTG-30which was essential for
the transcription of downstream target genes. Cysteine and glutamate act
as possible effectors of DnfR to activate the transcription of transcriptional
units of dnfG and dnfABCDE, respectively. This study provided new insights
in the transcriptional regulation mechanism of Dirammox by DnfR in
A. faecalis JQ135.
INTRODUCTION
Nitrogen is an essential component of all living organ-
isms and usually the main limiting nutrient for life on the
earth (Holmes et al., 2019; Kuypers et al., 2018). Micro-
bial ammonia oxidation plays an important role in the
nitrogen cycle (Kartal et al., 2011; Stein, 2011). Ammo-
nia can be oxidized in different microbial processes,
including nitrification, Anammox and Comammox
(Daims et al., 2015; Kessel et al., 2015; Kuenen, 2008;
Stein, 2011). Ammonia oxidation by heterotrophic bac-
teria has been reported a long time ago (Chen, Chen,
et al., 2021; Chen, Xu, et al., 2021; Huang et al., 2018;
Liu et al., 2015; Neerackal et al., 2016; Papen
et al., 1989; Shoda, 2017; Song et al., 2021), however,
its underlying molecular mechanism remains unfruitful
until recently that a new biological process called Dir-
ammox (direct ammonia oxidation, NH
3
!NH
2
OH!N
2
)
was identified in Alcaligenes species (Hou et al., 2022;
Wu et al., 2021; Xu, Qian, et al., 2022). A dinitrogen-
forming (dnf ) gene cluster was cloned from Alcaligenes
ammonioxydans strain HO-1. Escherichia coli cells
contains dnfABC genes converted ammonia to N
2
via
hydroxylamine (Wu et al., 2021). The dnfABC gene
cluster was further identified and characterized by
genetic deletion and complementary mutation in
Received: 14 November 2022 Accepted: 14 December 2022
DOI: 10.1111/1462-2920.16318
© 2022 Applied Microbiology International and John Wiley & Sons Ltd.
Environ Microbiol. 2022;114. wileyonlinelibrary.com/journal/emi 1
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Alcaligenes faecalis strain JQ135 (Xu, Qian,
et al., 2022). Recent in vitro enzymatic studies con-
firmed that DnfA could convert hydroxylamine into N
2
in
the presence of NADH and FAD (Wu et al., 2022).
Genomic survey in public databases showed that dnf
cluster was widely distributed in bacteria and responsi-
ble for Dirammox abilities (Hou et al., 2022).
MocR-like transcription factors (MocR-TFs) are a
subdivision of GntR family transcriptional regulators
and are distributed in both Gram-positive and Gram-
negative bacteria (Rigali et al., 2002; Tramonti
et al., 2018). MocR-TFs are chimeric proteins compris-
ing of an N-terminal winged helix-turn-helix DNA bind-
ing domain and a C-terminal aminotransferase-like
(AT-like) domain (Bramucci et al., 2011). To date, only
a few MocR-TFs have been characterized molecu-
larly, most of which are involved in the metabolism of
nitrogen-containing compounds. GabR, for example,
regulates transcription of γ-aminobutyric acid (GABA)
aminotransferase (GabT) gene and promotes the
catabolism of glutamate from GABA in Bacillus subtilis
(Al-Zyoud et al., 2015; Edayathumangalam
et al., 2013;Wuetal.,2017). PdxR, a transcriptional
regulator that activates transcription of the pdxST
genes encoding Pyridoxal 50-phosphate (PLP)
synthase in Bacillus clausii (Qaidi et al., 2013;
Tramonti et al., 2015). EhuR negatively regulated
ectoine uptake and catabolism in Sinorhizobium meli-
loti (Yu et al., 2016). Up to now, most of the reported
MocR-TFs control a single transcriptional unit. The
consensus sequence in the architecture of the DNA
binding sites of MocR-TFs has not been found
(Tramonti et al., 2018).
In the dnf cluster, a MocR-family transcriptional
gene dnfR was identified as an transcriptional activator
of dnfABC genes in A. faecalis JQ135 (Xu, Qian,
et al., 2022). However, the organization of dnf cluster
and its regulatory roles of DnfR on the entire dnf cluster
and on itself remain unclear. In the present study, the
function of DnfR was further investigated to better
understand the regulatory mechanism of Dirammox,
which expands the regulatory mechanism in the MocR-
like transcription factors (MocR-TFs).
EXPERIMENTAL PROCEDURES
Chemicals and media
All chemicals used for this experiment are commercially
available. Enzymes were purchased from Vazyme Bio-
tech. The heterotrophic nitrification medium (HNM)
used for bacteria cultivation was described as before
(Xu, Qian, et al., 2022). HNM2 medium was HNM with-
out carbon and nitrogen sources. Luria-Bertani
(LB) broth consisted of the following components:
tryptone (10.0 g/L), yeast extract (5.0 g/L), and NaCl
(10.0 g/L) at pH 7.0.
Bacterial strains and growth conditions
All bacterial strains and plasmids used in this study are
listed in Table 1.A. faecalis JQ135 was previously iden-
tified as an efficient nitrogen heterocyclic compounds
degrading bacterium (Mu et al., 2022; Qiu et al., 2018;
Zhang et al., 2018). E. coli strains were grown at 37C,
and other strains were grown at 30C. Media were sup-
plemented with ampicillin (Amp, 100 μg/ml), chloram-
phenicol (Cm 12.5 μg/ml), gentamicin (Gm, 50 μg/ml),
kanamycin (Km, 50 μg/ml), streptomycin (Str, 50 μg/ml),
or tetracycline (Tet, 40 μg/ml) as required.
Analytical methods
The concentrations of NH
4
+
and NO
2
were determined
by standard methods (APHA, 1998). Hydroxylamine
was determined according to the method of Frear and
Burrell (Frear & Burrell, 1955).
15
N
2
was determined by
GC/MS as previously reported (Xu, Qian, et al., 2022).
Bacterial cells were spectrophotometrically measured at
600 nm (OD
600
) (Wu et al., 2021).
Construction of plasmids and recombinant
strains JQ135ΔdnfR/dnfR
tr
The plasmid pBBR-dnfR
tr
which is 33 bp less than the
plasmid pBBR-dnfR was constructed for gene comple-
mentation. Gene dnfR
tr
was amplified using the primers
dnfRtr-F and dnfRtr-R and pBBR-dnfR used as the tem-
plate and then using the ClonExpress MultiS One Step
Cloning Kit (Vazyme Biotech), thus generating pBBR-
dnfR
tr
. The pBBR-dnfR
tr
plasmid was then transferred
into the JQ135ΔdnfR mutant to generate the comple-
mented strain JQ135ΔdnfR/dnfR
tr
. All primers were
listed in Table S1.
RNA extraction and RT-PCR
The method for culturing A. faecalis JQ135 and its
derivative strains, extraction and reverse transcription
of RNA from A. faecalis JQ135 and its derivative strains
was as described previously (Xu, Qian, et al., 2022).
The primers used for dnfIHRGABCDEF in this experi-
ment were described in Table S1. The transcriptional
level of the 16 S rRNA gene was used as internal stan-
dard, and the data in each column were calculated with
the 2
ΔΔCT
threshold cycle (C
T
) method using three
replicates. All samples were run in triplicates.
2XU ET AL.
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
TABLE 1 Strains and plasmids used in this study
Strains and plasmids Description Source
Strains
A. faecalis JQ135 Str
r
; wild type; metabolically versatile bacterium on nitrogen compounds (Xu, Qian,
et al., 2022)
JQ135ΔdnfR Str
r
,Km
r
;dnfR-deletion mutant of JQ135; dnfR::Km
r
(Xu, Qian,
et al., 2022)
JQ135ΔdnfR/dnfR Str
r
,Km
r
,Gm
r
; JQ135ΔdnfR containing pBBR-dnfR (Xu, Qian,
et al., 2022)
JQ135ΔdnfR/dnfR
tr
Str
r
,Km
r
,Gm
r
; JQ135ΔdnfR containing pBBR-dnfR
tr
This study
JQ135/pME6522-P
dnfA
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfA
This study
JQ135ΔdnfR/
pME6522-P
dnfA
Str
r
,Km
r
,Tc
r
; JQ135ΔdnfR containing pME6522-P
dnfA
This study
JQ135/pME6522-P
dnfH
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfH
This study
JQ135ΔdnfR/
pME6522-P
dnfH
Str
r
,Km
r
,Tc
r
; JQ135ΔdnfR containing pME6522-P
dnfH
This study
JQ135/pME6522-P
dnfG
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfG
This study
JQ135ΔdnfR/
pME6522-P
dnfG
Str
r
,Km
r
,Tc
r
; JQ135ΔdnfR containing pME6522-P
dnfG
This study
JQ135/pME6522-P
dnfR
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfR
This study
JQ135ΔdnfR/
pME6522-P
dnfR
Str
r
,Km
r
,Tc
r
; JQ135ΔdnfR containing pME6522-P
dnfR
This study
JQ135/pME6522-P
dnfR-m1
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfR-m1
This study
JQ135ΔdnfR/
pME6522-P
dnfR-m1
Str
r
,Km
r
,Tc
r
; JQ135ΔdnfR containing pME6522-P
dnfR-m1
This study
JQ135/pME6522-P
dnfR-m2
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfR-m2
This study
JQ135ΔdnfR/
pME6522-P
dnfR-m2
Str
r
,Km
r
,Tc
r
; JQ135ΔdnfR containing pME6522-P
dnfR-m2
This study
JQ135/pME6522-P
dnfR-m3
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfR-m3
This study
JQ135ΔdnfR/
pME6522-P
dnfR-m3
Str
r
,Km
r
,Tc
r
; JQ135ΔdnfR containing pME6522-P
dnfR-m3
This study
JQ135/pME6522-P
dnfH-m1
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfH-m1
This study
JQ135ΔdnfR/
pME6522-P
dnfH-m1
Str
r
,Km
r
,Tc
r
; JQ135ΔdnfR containing pME6522-P
dnfH-m1
This study
JQ135/pME6522-P
dnfH-m2
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfH-m2
This study
JQ135ΔdnfR/
pME6522-P
dnfH-m2
Str
r
,Km
r
,Tc
r
; JQ135ΔdnfR containing pME6522-P
dnfH-m2
This study
JQ135/pME6522-P
dnfH-m3
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfH-m3
This study
JQ135ΔdnfR/
pME6522-P
dnfH-m3
Str
r
,Km
r
,Tc
r
; JQ135ΔdnfR containing pME6522-P
dnfH-m3
This study
JQ135/pME6522-P
dnfG2
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfG2
This study
JQ135/pME6522-P
dnfG3
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfG3
This study
JQ135/pME6522-P
dnfG4
Str
r
,Tc
r
; JQ135 containing pME6522-P
dnfG4
This study
DH5αCloning host Lab stock
HB101(pRK2013) Help strain for parental mating Lab stock
Plasmids
pBBR1MCS-5 Gm
r
; broad-host-range cloning plasmid Lab stock
pMD19-T Cloning plasmid Takara
pCE2 TA/Blunt-Zero Cloning plasmid for transcriptional start site Vazyme
pBBR-dnfR Gm
r
; pBBR1MCS-5 harbouring dnfR gene (Xu, Qian,
et al., 2022)
pBBR-dnfR
tr
Gm
r
; pBBR1MCS-5 harbouring dnfR
tr
gene This study
pET-dnfR Km
r
; NdeI-XhoI fragment containing dnfR inserted into pET29a(+) This study
(Continues)
MocR FAMILY TRANSCRIPTIONAL REGULATOR DnfR HAS MULTIPLE BINDING 3
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
EMSA
All DNA fragments used in EMSA were PCR amplified
from A. faecalis JQ135 genomic DNA using the primers
shown in Table S1. Approximately 20 ng of a promoter
probe was mixed with 140 nM purified DnfR in a binding
buffer (50 mM TrisHCl [pH 7.0], 30 mM KCl, 5% [vol/vol]
glycerol, 1 mM EDTA, and 5 mM DTT). The effects of
ammonia, hydroxylamine, nitrite, nitrate and 20 essential
amino acids on the binding of DnfR to the promoter
probes were evaluated by adding 0.1 mM of these sub-
strate to the reaction system respectively. The mixture
was incubated at 25C for 30 min and was then sepa-
rated by 6% (vol/vol) native polyacrylamide gel electro-
phoresis in 0.5Tris-glycine-EDTA. Gels were stained
with 4 S Green Plus Nucleic Acid Stain (Sangon Biotech),
and DNA fragments were visualized under UV light.
DNase I footprinting
The promoter region P
dnfG
(F
cl
-2) and P
dnfH-dnfR
(Fb) were PCR amplified and inserted into the plasmid
pMD19-T (TaKaRa) to create the plasmids pMD19T-Fb
and pMD19T-F
cl
-2, respectively. Then the specific
method for DNase I footprinting was described as
before (Xu, Qian, et al., 2022).
β-galactosidase assays
The primers of lacZ-dnfH/R/G-PstI/EcoRI listed in the
TableS1wereusedtoamplifiedthefragmentsof
promoters of the dnfH/R/Gto create the plasmids of
pME6522-P
dnfH/R/G
-lacZ. The primers of lacZ-P
dnfH/R-
m1/2/3
-PstI/EcoRI were used to amplified the fragments
of mutated promoters of the dnfH/Rto create the of a
series of mutated plasmids, in which, the nucleotide
Gwas exchanged with A; the nucleotide Twas
exchanged with C. The primers of lacZ-P
dnfG2/3/4
-
PstI/EcoRI were used to amplified the different length
of fragments containing the promoters of the dnfG to
create the plasmids of pME6522-P
dnfG2/3/4
-lacZ.Take
P
dnfG
for example. The PCR products were digested
with EcoRI and PstI and ligated into the EcoRI/PstI-
digested pME6522 to generate plasmid
pME6522-P
dnfG
. The resulting plasmids containing
P
dnfG
-lacZ fusions were transformed into A. faecalis
JQ135 and JQ135ΔdnfR, yielding JQ135/
pME6522-P
dnfG
and JQ135ΔdnfR/pME6522-P
dnfG
,
respectively. The plasmids of pME6522-P
dnfH/R-m1/2/3
and pME6522-P
dnfG2/3/4
were only transformed into
strain A. faecalis JQ135. β-galactosidase assays were
performed as before (Xu, Qian, et al., 2022). One
Miller unit of enzyme activity was defined as the
amount of enzyme required to catalyse o-nitrophenyl-
β-D-galactopyranoside to produce 1 μmol o-
nitrophenol per min (Sambrook & Russell, 2001). All
samples were tested in triplicates.
Transcriptional start site of the dnf cluster
The transcriptional start sites (TSSs) of the dnfH,dnfR
and dnfG genes were determined by 50-rapid amplifica-
tion of cDNA ends (50RACE) using the HiScript-TS 50/30
TABLE 1 (Continued)
Strains and plasmids Description Source
pME6522 Tc
r
; shuttle vector for transcriptional lacZ fusion and promoter probing Lab stock
pME6522-P
dnfA
Tc
r
;P
dnfA
fragment fused into pME6522 This study
pME6522-P
dnfH
Tc
r
;P
dnfH
fragment fused into pME6522 This study
pME6522-P
dnfR
Tc
r
;P
dnfR
fragment fused into pME6522 This study
pME6522-P
dnfG
Tc
r
;P
dnfG
fragment fused into pME6522 This study
pME6522-P
dnfR-m1
Tc
r
;P
dnfR-m1
fragment fused into pME6522 This study
pME6522-P
dnfR-m2
Tc
r
;P
dnfR-m2
fragment fused into pME6522 This study
pME6522-P
dnfR-m3
Tc
r
;P
dnfR-m3
fragment fused into pME6522 This study
pME6522-P
dnfH-m1
Tc
r
;P
dnfH-m1
fragment fused into pME6522 This study
pME6522-P
dnfH-m2
Tc
r
;P
dnfH-m2
fragment fused into pME6522 This study
pME6522-P
dnfH-m3
Tc
r
;P
dnfH-m3
fragment fused into pME6522 This study
pME6522-P
dnfG2
Tc
r
;P
dnfG2
fragment fused into pME6522 This study
pME6522-P
dnfG3
Tc
r
;P
dnfG3
fragment fused into pME6522 This study
pME6522-P
dnfG4
Tc
r
;P
dnfG4
fragment fused into pME6522 This study
pMD19T-Fb Amp
r
; 248-bp fragment, promoter region of dnfR and dnfH, directionally cloned into
pMD19-T
This study
pMD19T-F
cl
-2 Amp
r
; 184-bp fragment, promoter region of dnfG, directionally cloned into pMD19-T This study
4XU ET AL.
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
RACE kit (Vazyme Biotech) according to the manufac-
turers instructions. Total RNA was used and isolated
as described above. The primers TSS-dnfA/R/H/G-1/2
used in this experiment were listed in the Table S1. The
final PCR product was purified with a gel-extraction kit
(Vazyme Biotech) and then ligated into pCE2 TA/Blunt-
Zero vector using the Blunt-Zero Cloning kit (Vazyme
Biotech) for sequencing. The promoters region of the
four transcriptional units are predicted through the fol-
lowing websites: phiSITE (http://www.phisite.org/main/
index.php?nav=tools&nav_sel=hunter) (Klucar
et al., 2009), BacPP (http://www.bacpp.bioinfoucs.com/
home/) (Silva et al., 2011) and BDGP (https://www.
fruitfly.org/seq_tools/promoter.html) (Reese, 2002).
RESULTS
Organization and transcriptional analysis
of the dnf cluster
Our previous studies have shown that dnfABC and
dnfR genes were essential for Dirammox process (Xu,
Qian, et al., 2022). However, the composition of the dnf
cluster was not experimentally investigated. According
to the previous investigation about the dnfABCR genes,
RT-PCR was carried out to investigate the entire dnf
cluster (Figure 1). Total RNA, cDNA and DNA extrac-
tion from the JQ135 cells were used as the templates
for PCR amplification. The amplified products were
detected by electrophoresis to determine the transcripts
of dnf clusters. As shown in Figure 1B, among the
amplified 11 fragments (2 fragments within genes and
9 fragments across genes), 10 fragments were suc-
cessfully amplified using cDNA as the template except
fragment 5. Therefore, the dnfABC genes were co-
transcribed with two downstream genes (named as
dnfDE). On the other side, two genes (named dnfIH)
opposite to dnfR form a transcription unit. Interestingly,
fragment F3 can also be amplified, which means that
the four genes (named dnfIHRG) seem to be co-tran-
scribed, though dnfR and dnfIHG are divergently orien-
tated. The possible reason might be that the
transcription unit dnfIHRG was also started by the pro-
moter of dnfG (see below). Therefore, the dnf cluster
was organized into five transcriptional units, that is,
FIGURE 1 Tanscriptional analysis of dnf cluster. (A) Organization of dnf cluster. The gene IDs of dnfI to dnfF are AFA_14070 to
AFA_14115, respectively. (B) Transcriptional unit analysis of the dnf gene cluster. PCR amplification of the dnf gene cluster using total RNA (R),
cDNA (cD) and DNA (D) as the templates. The amplified products were detected by electrophoresis. (C) Transcriptional analysis of dnfI,dnfH,
dnfR,dnfG,dnfA,dnfB,dnfC,dnfD,dnfE and dnfF in strains JQ135, JQ135ΔdnfR, JQ135ΔdnfR/dnfR in HNM. Different letters indicate
differences as determined by one-way AVONA (p< 0.05). (D) In vivo dnfH,dnfR,dnfG and dnfA promoter activity assay. β-galactosidase assays
were performed with JQ135 and JQ135ΔdnfR, carrying the plasmids pME6522P
dnfH
, pME6522P
dnfR
, pME6522P
dnfG
and pME6522P
dnfA
,
respectively, grown in the HNM. P
dnfH
or P
dnfR
is a 155 bp promoter region of dnfH or dnfR, respectively. P
dnfG
or P
dnfA
is a 301 or 381 bp
promoter region of dnfG or dnfA, respectively. β-galactosidase activity was measured as described in materials and methods. Each value is the
mean ± standard deviation (SD) of at least three cultures. Different letters indicate differences as determined by one-way AVONA (p< 0.05)
MocR FAMILY TRANSCRIPTIONAL REGULATOR DnfR HAS MULTIPLE BINDING 5
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
dnfHI,dnfR,dnfG,dnfABCDE and dnfF (Figure 1A).
DnfI and DnfG were predicted as serine hydroxymethyl-
transferase while DnfH is described as phosphoserine
aminotransferase. DnfD, DnfE and DnfF are annotated
as pyridoxal kinase, high-affinity choline uptake protein
BetT and redox-sensitive transcriptional activator
SoxR, respectively.
The transcriptions of dnf cluster genes in strain
JQ135 were assessed using quantitative RT-PCR (RT-
qPCR). As shown in Figure 1C, when cultured in HNM,
the transcription levels of 10 dnf genes in strain JQ135
were 35.2 ± 1.5, 15.0 ± 0.8, 5.4 ± 0.6, 8.3 ± 0.8, 248.0
± 5.2, 150.1 ± 2.5, 27.0 ± 0.6, 8.1 ± 0.5, 9.2 ± 1.0 and
4.8 ± 0.4 folds higher, respectively, than those in
JQ135ΔdnfR (Figure 1C). In the complemented strain
JQ135ΔdnfR/dnfR, the transcription levels of 10 dnf
genes were similar to those of the wild-type strain
JQ135. These results indicated that these 10 genes
constitute a cluster regulated by DnfR.
Identification of the transcription start sites
of transcriptional units of dnfIH,dnfR,
dnfG, and dnfABCDE
In our previous study, we determined the TSS of dnfA
gene (Xu, Qian, et al., 2022). In this study, we contin-
ued to use the total RNA extracted from JQ135 cells
grown in HNM to determine the TSSs of other three
transcriptional units in the dnf cluster by 50RACE. As
shown in Figure 2, the A bases of the ATG start codons
of dnfH,dnfR and dnfG are determined at positions
25, 13 and 89, respectively, relative to their TSSs. A
more detailed analysis of the promoter is shown in
Figure 2. The TSSs of these two set of divergent tran-
scriptional units do not overlap with each other. The
TSSs of dnfH and dnfR genes are close (88 bp), while
the TSSs of dnfG and dnfA genes are separated by a
distance of 300 bp. A more detailed analysis of the four
promoters is shown in Figure 2.
Determination of the binding sites of DnfR
Previous study has showed that DnfR bound to the
upstream region of promoter region of dnfABC genes
and activated its transcriptional expression (Xu, Qian,
et al., 2022). Here, further studies were carried out to
investigate the regulatory mechanism and other pos-
sible binding regions of DnfR. Five intergenic frag-
ments that may contain promoter region with a long
interval in the 10 genes were selected, namely dnfI-
dnfH (fragment Fa, 241 bp), dnfH-dnfR (fragment Fb,
248 bp), dnfG-dnfA (fragment Fc, 688 bp), dnfD-dnfE
(fragment Fd, 227 bp) and the promoter region of dnfF
(fragment Fe, 349 bp). The purified DnfR was tested
for its ability to bind to the above five DNA fragments
using electrophoretic mobility shift assay (EMSA).
Figure 2D showed that fragments Fb and Fc were
shifted while fragments Fa, Fd and Fe were not. In the
fragment Fc, DnfR has been shown to bind to the pro-
moter region of dnfA. Since fragment Fc was a long
space with two divergent genes (dnfG and dnfA), we
further tested whether DnfR could bind to the pro-
moter region of dnfG (206 to +95 relative to the
dnfG TSS, F
cl
) alone. Fragment F
cl
were then subdi-
vided into two subfragments F
cl
-1 to F
cl
-2. EMSA
results in Figure 2E showed that F
cl
and subfragment
F
cl
-2 were shifted in the presence of DnfR, indicating
the presence of DnfR binding site in the promoter
region of dnfG. DNase I footprinting was performed to
identify the DnfR-binding sites of above intergenic
regions fragment Fb and F
cl
-2 (Figure 2). In the dnfH-
dnfR intergenic sequence, DnfR binds to a 48-bp
region which located on the 14 to 34 and 54 to
102 according to the TSSs of dnfR and dnfH,
respectively. In the promoter region of dnfG,DnfR
binds to the 108 to 144 region according to the
TSS of dnfG. A more detailed analysis of the four pro-
moters is shown in Figure 2.
The intact dnfR gene is required for
regulation of Dirammox
As shown in Figure 2A, the binding region towards frag-
ment F
2
covered the A base of ATG of dnfR gene
(1506 bp). Then, a second start codon ATG was found
with 33 bp space downstream the dnfR gene. In order
to check which ATG is the true starting codon, the trun-
cated dnfR
tr
(1473 bp) was supplemented to mutant
strain JQ135ΔdnfR. A new complementary strain
named as JQ135ΔdnfR/dnfR
tr
was constructed. The
results showed that JQ135ΔdnfR/dnfR
tr
had no differ-
ences to JQ135ΔdnfR (Figure S1). These experiments
indicated that the 33 bp sequence of dnfR is
necessary.
The role of DnfR and the conserved
sequences of three binding sites
To verify the roles of these binding regions on transcrip-
tion of dnf genes, a series of promoter fragments con-
taining DnfR protection regions were fused with lacZ
gene and inserted to plasmid pME6522, produced plas-
mids pME6522-P
dnfA
, pME6522-P
dnfG
, pME6522-P
dnfH
,
and pME6522-P
dnfR
, and then transformed them into
strains JQ135 and JQ135ΔdnfR, respectively. The
β-galactosidase assays showed that, similar to dnfA,
promoters of dnfIH and dnfG showed no activities in
mutant strain JQ135ΔdnfR, while expressed high activi-
ties (3.5 ± 0.4, 4.9 ± 0.8 folds higher at 12 h than in
JQ135ΔdnfR) in wild type strain JQ135 (Figure 1D),
6XU ET AL.
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
suggesting that DnfR actively regulates the transcrip-
tions of transcriptional units of dnfIH,dnfG and
dnfABCDE. In contrast, β-galactosidase activities of
promoter P
dnfR
in JQ135ΔdnfR were approximately
11.6 ± 0.9 fold at 12 h relative to those in wide type
JQ135, indicating that DnfR negatively regulated itself.
FIGURE 2 Identification of DnfR binding sites. (A) The DNA elements in the promoter regions of dnfH and dnfR. The TSSs of dnfH and dnfR
are indicated in grey and red, respectively, and are indicated with arrowheads. The DNA binding sites of DnfR are shown in purple.
(B) Organization of dnf cluster. The figures below the cluster are fragments used in the EMSA experiments. (C) DNA elements in the promoter
region of dnfG and dnfA. The TSSs of dnfG and dnfA are indicated in grey and green, respectively, and are indicated with arrowheads. The
subfragments used in the EMSA experiments are indicated. The DNA binding sites of DnfR are shown in purple. (D) EMSAs of fragments Fa, Fb,
Fc, Fd and Fe with purified DnfR (140 nM). (E) EMSAs of subfragments F
cl
,F
cl
-1 and F
cl
-2 with purified DnfR (140 nM). (F) and (G) DNase I
footprinting determination of the protected regions in P
dnfH
-
dnfR
and P
dnfG
promoter regions by DnfR, respectively. The DnfR protected regions
were shown in dashed box and the sequence were shown at the bottom
MocR FAMILY TRANSCRIPTIONAL REGULATOR DnfR HAS MULTIPLE BINDING 7
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Comparing three DnfR binding sites of promoter
regions of dnfA,dnfG, and dnfH genes, they share a
consensus sequence of 6-bp direct repeats GGTCTG-
N
17
-GGTCTGwith 17 bp spacer and located upstream
of the TSSs (Figure 3A). In addition, there are also two
sets of perfect palindrome sequences 50-GGTCTG-
N
6
(N
29
)-CAACAC-30in the DnfR binding site in frag-
ment F
2
(intergenic region of dnfH-dnfR), with the inter-
vals of 6 and 29 bp, respectively. In order to determine
the roles of repeats sequences and palindromes
sequences in the promoters, a series of site-directed
mutations (site1, site2, or site3 in Figure 3) of intergenic
region of dnfH-dnfR were ligated into the EcoRI/PstI-
digested pME6522 to generate plasmids
pME6522-P
dnfR-m1
to P
dnfR-m3
(to test the activity of
dnfR promoter) and pME6522-P
dnfR-m4
to P
dnfR-m6
(to test the activity of dnfH promoter) (Figure 3), and
then transformed into wide type JQ135 and mutant
JQ135ΔdnfR, respectively. β-galactosidase activities
driven by P
dnfR-m1
and P
dnfR-m2
promoters in wide type
were 16.9 ± 1.3, 19.2 ± 1.7 fold higher at 12 h than
those in JQ135ΔdnfR, respectively, which are similar to
those by P
dnfR
(in the wide type 11.6 ± 0.9 fold higher
at 12 h than in JQ135ΔdnfR). Very low β-galactosidase
activity (<60 Miller units) of P
dnfR-m3
promoter were
detected at 12 both in strain JQ135 and JQ135ΔdnfR.
Next, the β-galactosidase activities driven by P
dnfH-m3
promoter in wild type JQ135 were 8.6 ± 1.1 fold higher
FIGURE 3 Features and characterizations of three binding sites of DnfR. (A) Analysis of the three binding sites. The conserved areas of
three binding sites are indicated in blue or orange and marked by vertical lines. (B) Mutational analysis of the binding site of P
dnfH-dnfR
. Mutational
sites are indicated in dotted line. (C) β-galactosidase assays were performed with JQ135 and JQ135ΔdnfR, carrying the plasmids pME6522
P
dnfH
, pME6522P
dnfR
and a series of mutant plasmids grown in the HNM. Each value is the mean ± standard deviation (SD) of at least three
cultures. Different letters indicate differences as determined by one-way AVONA (p< 0.05)
8XU ET AL.
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
at 12 h than those in JQ135ΔdnfR, which are similar to
P
dnfH
(9.1 ± 0.7 fold higher at 12 h in the wide type than
those in JQ135ΔdnfR); while very low β-galactosidase
activity (<80 Miller units) of P
dnfH-m1
and P
dnfH-m2
pro-
moters were detected at 12 both in strain JQ135 and
JQ135ΔdnfR. These results indicated that the two
direct repeated sequences (site1 and site2, blue parts
in Figure 3) were essential for the activation of the
downstream target genes but has no effect on its
upstream dnfR gene. In contrast, the reverse palin-
drome sequence (site3, orange parts in Figure 3), it
had no effect on the target genes, but was crucial for
the expression of dnfR itself.
Genes dnfGRHI forms as a
transcriptional unit
Figure 2shows that dnfR and dnfIH areasetofdiver-
gently orientated transcriptional units, and their tran-
scription start sites do not overlap, however, RT-PCR
analysis showed that dnfR is co-transcribed with dnfH
(Figure 1). Therefore, it is hypothesized that the pro-
moter of dnfG could transcribe dnfGRHI together. To
verify this hypothesis, a series of fragments with/
without the dnfG promoter but not reaching to the 10
region of gene dnfH were ligated into the
β-galactosidase reporter plasmids pME6522.
β-galactosidase activities driven by P
dnfG2
and P
dnfG3
promoters in wide type JQ135 were 5.5 ± 0.4, 4.7
± 0.4 fold higher at 12 h than those in JQ135ΔdnfR,
respectively, which are similar to P
dnfG
; while very low
β-galactosidase activity (<100 Miller units) of P
dnfG4
plasmids were detected at 12 both in strain JQ135
and JQ135ΔdnfR (Figure 4). The results indicated that
the P
dnfG
was a promoter of transcriptional unit cover-
ing the intergenic region of dnfH-dnfR genes, that is,
dnfGRHI formed as a transcriptional unit.
The possible effectors of DnfR
To explore the possible effectors of DnfR towards dnf
cluster, the EMSA and/or β-galactosidase assays were
performed. EMSA experiments showed that 0.1 mM
ammonia, hydroxylamine, nitrite, and nitrate had no sig-
nificant effects on DnfR binding to the four promoter
regions (P
dnfH-m3
,P
dnfR-m2
,P
dnfG
and P
dnfA
), inferring
that none of them is the efficient effector for DnfR
(Figure S2). Then 20 amino acids were used to investi-
gate whether they were the possible effectors. As shown
in the Figure 5, none of the 20 amino acids (0.1 mM)
could increase the binding of P
dnfH-m3
or P
dnfR-m2
frag-
ments with DnfR, indicating that 20 amino acids may not
be the possible effectors/ligands of DnfR to activate dnfH
or dnfR gene. However, 0.1 mM cysteine and glutamate
could increase the binding of DnfR towards P
dnfG
and
P
dnfA
fragment, respectively (Figure 5). In addition, the
amount of DnfRP
dnfG
and DnfRP
dnfA
complex
increased along with the gradient concentration of cyste-
ine and glutamate, respectively (Figure 5I,J). Further-
more, the effects of cysteine and glutamate to DnfR
were investigated using four β-galactosidase activity
reporter plasmids pME6522-P
dnfA
, pME6522-P
dnfG
,
pME6522-P
dnfH
, and pME6522-P
dnfR
into strain JQ135.
The strains were then cultured in HNM2 (HNM without
carbon and nitrogen source) with or without 1 mM cyste-
ine or glutamate. As shown in Figure 6,verylow
β-galactosidase activity (<200 Miller units) of all four
reporter plasmids were detected at 4 or 8 h in strain
JQ135 in HNM2, indicating no transcriptions when no
carbon and nitrogen sources were present in media.
Next, the level of β-galactosidase of pME6522-P
dnfA
were approximately 2.8 ± 0.5 times (317 ± 9.2 Miller
units) higher at 4 or 8 h induced by glutamate than cyste-
ine or HNM2. Furthermore, β-galactosidase activities of
pME6522-P
dnfG
were 12.1 ± 1.3 times (1742 ± 69
Miller units) and 10.1 ± 1.8 times (1452 ± 41 Miller units)
higher at 4 or 8 h induced by glutamate or cysteine than
that in HNM2, respectively. In contrast, neither glutamate
nor cysteine could induce the expression of the
pME6522-P
dnfR
and -P
dnfH
(β-galactosidase activities
FIGURE 4 In vivo dnfG,dnfG-dnfR,dnfG-dnfH and dnfR-P
dnfH
promoter activity assays. (A) Schematic diagram of the promoter
regions of dnfG,dnfG-dnfR,dnfG-dnfH and dnfR-P
dnfH
. (B) β-
galactosidase assays were performed with JQ135 and JQ135ΔdnfR,
carrying the plasmids pME6522P
dnfG
, pME6522P
dnfG2
, pME6522
P
dnfG3
and pME6522-P
dnfG4
, respectively, grown in the HNM. P
dnfG
,
P
dnfG2
,P
dnfG3
and P
dnfG4
are 301, 1766, 3381 and 389-bp promoter
regions of dnfG, respectively. β-galactosidase activity was measured
as described in materials and methods. Each value is the mean
± standard deviation (SD) of at least three cultures. Different letters
indicate differences as determined by one-way AVONA (p< 0.05)
MocR FAMILY TRANSCRIPTIONAL REGULATOR DnfR HAS MULTIPLE BINDING 9
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
FIGURE 5 Determination of effectors of DnfR. (A, B), (C, D), (E, F), and (G, H) are EMSA with P
dnfH-m3
,P
dnfR-m2
,P
dnfG
, and P
dnfA
promoter
sequences (20 nM), respectively, and DnfR (140 nM) in the presence of 0.1 mM 20 amino acids. (): DNA fragment (10 nM) alone: (+): DNA
fragment (10 nM) plus DnfR; (+amino acid) DNA fragment (10 nM) plus DnfR and amino acid. (I) EMSA with P
dnfG
promoter sequence (20 nM)
and DnfR (140 nM) in the presence of different concentrations of cysteine. (J) EMSA with P
dnfA
promoter sequence (20 nM) and DnfR (140 nM)
in the presence of different concentrations of glutamate
10 XU ET AL.
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
<200 Miller units) (Figure 6). Based on the results of
EMSA and β-galactosidase assays, cysteine and gluta-
mate could be the effectors of transcriptional units of
dnfG and dnfABCDE,respectively.
DISCUSSION
The present study investigated the organization of dnf
gene cluster in A. faecalis JQ135, and expanded it as
five transcriptional units: dnfHI,dnfR,dnfG,dnfABCDE,
and dnfF. EMSA and DNase I footprinting analyses
showed that DnfR could activate the transcriptions of
dnfHI,dnfG, and dnfABCDE genes but repress the
transcription itself. The three binding sites of DnfR
shared a 6-bp repeated conserved sequence 50-
GGTCTG-N
17
-GGTCTG-30. The cysteine and gluta-
mate could be the effectors of transcriptional units of
dnfG and dnfABCDE, respectively.
MocR-TFs belongs into the GntR-family transcrip-
tional regulators (Taw et al., 2015; Xu, Qian,
et al., 2022). MocR-TFs are special in its chimeric struc-
ture, which consist of an N-terminal DNA-binding
domain and a C-terminal aspartate aminotransferase-
like domain (Bramucci et al., 2011). However, no
reports on its aspartate aminotransferase activities has
been found ever. They often involves in controlling the
metabolism of organic nitrogen compounds
(Belitsky, 2014; Tramonti et al., 2016; Wu et al., 2017).
Previous studies showed that most MocR-TFs encod-
ing genes and their target genes are located together
with divergent orientations. The promoters of the two
genes are located in the intergenic region, and often
overlap with each other. MocR-TFs binds this region to
represses its own expression, but activates the expres-
sion of the structure genes. For example, GabR, regu-
lating GABA metabolism in Bacillus subtilis,isan
autorepressor and transcriptional activator of gabR and
gabT, respectively, which allows the bacterium to use
GABA as nitrogen and carbon sources (Okuda
et al., 2014; Wu et al., 2017). PdxR, involved in the reg-
ulation of pyridoxal phosphate synthesis in Bacillus
clausii, activates the transcription of pdxST genes
encoding PLP synthase while represses its own
expression (Tramonti et al., 2015). However, MocR-
TFs binding to multiple transcriptional units or distant
genes are rarely reported. In this study, DnfR controls
multiple sites of dnf gene cluster in A. faecalis JQ135,
that is, one site in the spacer region of dnfH and dnfR
and two sites in the spacer region of dnfG and dnfA.
These findings of multiple regulatory sites provided
new research paradigm of MocR-TFs.
In previous studies, the binding sites of MocR-TFs
are diverse in DNA length, sequence, and arrange-
ments (Tramonti et al., 2018). In this study, a conserved
sequence of 6-bp direct repeats 50-GGTCTG-N
17
-
GGTCTG-30were shared with three DnfR binding sites
which were essential for the activation of the down-
stream target genes (Figure 4). No binding sequences
of MocR-TFs were identical to this. The most similar
MocR-TFs target DNA was 50-ATACCA-N
34
-ATACCA-
30for GabR binding. The common feature was ACC but
the sequences were reverse complementary, that is,
GGT in DnfR. Nevertheless, some broad common fea-
tures can be drawn out. Like TauR, PdxR and EhuR, a
relevantly common feature is the occurrence of a TG
group of DnfR (Tramonti et al., 2015; Wiethaus
et al., 2008; Yu et al., 2016); Another is the 23 bp dis-
tance of the two direct repeats of DnfR, which is similar
to most MocR-TFs (Tramonti et al., 2018). In addition,
the structure of two direct repeats in binding sites of
MocR-TFs was similar with findings in AraC/XylS family
transcription regulators (Gallegos et al., 1997;
Schleif, 2010). For example, AraC binds a tandem
repeat 50-AGC-N
7
-TCCATA-30motif to activate the
expression of araBAD genes which involved in the
catabolism of L-arabinose; XylS binding sites were two
essential repeat motifs 50-T(C/A)CA-N
4
-TGCA-30which
involved in toluate degradation (Gallegos et al., 1997).
These structural features of direct repeats contrast with
binding sites by members of IclR (Molina-Henares
et al., 2005), LysR (Maddocks & Oyston, 2008), SoxR
(Wang et al., 2021) and TetR (Bertram et al., 2021;
Ramos et al., 2005) family regulators, which recognize
palindromic or inverted repeat sequences.
The dnfABC genes are responsible for the conver-
sion of ammonia into N
2
via NH
2
OH and considered as
widely distribution in bacteria. Lasted research showed
that DnfABC can enzymatically convert NH
2
OH into N
2
in vitro (Wu et al., 2022). However, the biological pro-
cess of transforming ammonia into NH
2
OH still remains
FIGURE 6 Effects of cysteine and glutamate on four promotors.
β-galactosidase assays were performed with JQ135 carrying the
P
dnfH
-lacZ,P
dnfR
-lacZ,P
dnfG
-lacZ and P
dnfA
-lacZ transcriptional
fusions grown in the presence of 0.5 mM cysteine or glutamate at 0, 4
and 8 h. Each value is the mean ± standard deviation (SD) of at least
three cultures. Different letters indicate differences as determined by
one-way AVONA (p< 0.05)
MocR FAMILY TRANSCRIPTIONAL REGULATOR DnfR HAS MULTIPLE BINDING 11
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
mystery. The results of this study showed that
10 genes, including dnfABC gene and dnfDEFGHIR,
formed a gene cluster and were regulated by DnfR.
The dnfDEGI genes are predicted to be involved in
nitrogen-related metabolism. For example, DnfI and
DnfG were predicted as serine hydroxymethyltransfer-
ase while DnfH is described as phosphoserine amino-
transferase. Although the functions of the other seven
genes were not fully identified or investigated
(e.g., gene deletion and complementation) in this study,
we might infer that dnfDEFGHI genes must participate
in the Dirammox process in a certain way. At the same
time, glutamate or cysteine may interact with DnfR to
activate the expression of dnfABCDE and dnfHI.On
this basis, it is possible that the true substrate(s) of Dnf
is nitrogen-containing organic compound(s) but not
ammonia itself. Another possibility is that the Dirammox
is deeply intertwined with primary metabolism
(e.g., amino acid synthesis or degradation), which
increasing the difficulty and complexity to investigate.
During the regulatory processes by transcriptional
proteins, specific effectors or inducers are generally
needed. For example, PLP and GABA trigger GabR-
mediated transcription activation in Bacillus subtilis via
inducing the expression of gabT genes (Wu
et al., 2017); the transcription of transcriptional units of
genKH and genDFM in Corynebacterium glutamicum
can be activated by GenR in the present of effectors
3-hydroxybenzoate or gentisate (Chao & Zhou, 2013);
1-Naphthol as effector to activate mcbBCDEF cluster
transcription encoding the upstream pathway of carba-
ryl degradation in Pseudomonas sp. strain XWY-1 (Ke
et al., 2021). The β-galactosidase activity assays in
Figure 6of this study showed that no promotor activi-
ties were detected in wild-type strain JQ135 when no
carbon and nitrogen sources were present in media,
indicating that the transcription of dnfR,dnfA,dnfG and
dnfH required effectors or inducers. EMSA analyses
showed that 0.1 mM ammonia, hydroxylamine, nitrite,
and nitrate had no significant effect on DnfR binding to
all four promoter regions (Figure S2), suggesting that
none of them is the direct effector for DnfR. The cyste-
ine and glutamate could activate the expression of
dnfG and dnfA genes, respectively, but neither of them
have effects on the expression of dnfH gene. Moreover,
DnfR could repress its own expression and its tran-
scription may not depend on glutamate and cysteine.
Therefore, we may infer that the effectors of DnfR
towards four dnf transcriptional units are different with
each other. Some regulator protein can control multiple
sites using one effector. For example, gentisate can
induce GenR to activate transcriptions of two transcrip-
tional units (genD and genK)inC. glutamicum, while
6-hydroxypicolinic acid can derepress transcriptions of
three transcriptional units (picT,picB and picC) from
PicR in A. faecalis (Chao & Zhou, 2013; Xu, Wang,
et al., 2022). Why are there multiple binding sites of
DnfR in the dnf cluster with different effectors? The
probable reasons might be that these transcriptional
units in the dnf cluster are expressed at different time
or in different order, and response for different effec-
tors, in order to regulate itself more finely to adapt
changing surroundings, nutrients or stresses. These
hypotheses need further deep studies.
AUTHOR CONTRIBUTIONS
Siqiong Xu: Data curation (equal); investigation (equal);
writing original draft (equal); writing review and edit-
ing (equal). Xiao Wang: Investigation (equal). Lu Xu:
Investigation (equal). Kexin Wang: Investigation
(equal). Yinhu Jiang: Investigation (equal). Fuyin
Zhang: Investigation (equal). Qing Hong: Funding
acquisition (equal); investigation (equal). Jian He: Fund-
ing acquisition (equal); investigation (equal); supervision
(equal); writing original draft (equal); writing review
and editing (equal). Shuang-Jiang Liu: Conceptualiza-
tion (equal); funding acquisition (equal); investigation
(equal); project administration (equal); writing original
draft (equal); writing review and editing (equal). Jiguo
Qiu: Conceptualization (equal); funding acquisition
(equal); investigation (equal); project administration
(equal); supervision (equal); writing original draft
(equal); writing review and editing (equal).
ACKNOWLEDGEMENTS
This work was supported by grants from the National
Key R&D Program of China (2019YFA0905500) and
the National Natural Science Foundation of China
(No. 32070092 and 32170128).
CONFLICT OF INTEREST
The authors declare that they have no conflict of
interest.
DATA AVAILABILITY STATEMENT
The complete genome sequence of Alcaligenes faeca-
lis JQ135 is available in GenBank at accession number
CP021641. The gene IDs of dnfI to dnfF are
AFA_14070 to AFA_14115, respectively.
ORCID
Qing Hong https://orcid.org/0000-0001-5385-6281
Shuang-Jiang Liu https://orcid.org/0000-0002-7585-
310X
Ji-Guo Qiu https://orcid.org/0000-0002-7633-6227
REFERENCES
Al-Zyoud, W.A., Hynson, R.M., Ganuelas, L.A., Coster, A.C., Duff, A.P.,
Baker, M.A. et al. (2015) Binding of transcription factor GabR to
DNA requires recognition of DNA shape at a location distinct from
its cognate binding site. Nucleic Acids Research, 44, 14111420.
APHA. (1998) Standard methods for the examination of water and
wastewater. 20th edition. Washington DC: American Public
Health Association, American Water Works Association and
Water Environmental Federation.
12 XU ET AL.
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Belitsky, B. (2014) Role of PdxR in the activation of vitamin B6 bio-
synthesis in listeria monocytogenes.Molecular Microbiology, 92,
11131128.
Bertram, R., Neumann, B. & Schuster, C.F. (2021) Status quo of tet
regulation in bacteria. Microbial Biotechnology, 15, 11011119.
Bramucci, E., Milano, T. & Pascarella, S. (2011) Genomic distribution
and heterogeneity of MocR-like transcriptional factors containing
a domain belonging to the superfamily of the pyridoxal-50-
phosphate dependent enzymes of fold type I. Biochemical and
Biophysical Research Communications, 415, 8893.
Chao, H.-J. & Zhou, N.-Y. (2013) GenR, an IclR-type regulator, acti-
vates and represses the transcription of gen genes involved in
3-Hydroxybenzoate and gentisate catabolism in Corynebacte-
rium glutamicum.Journal of Bacteriology, 195, 15981609.
Chen, J., Xu, J., Zhang, S., Liu, F. & Wu, J. (2021) Nitrogen removal
characteristics of a novel heterotrophic nitrification and aerobic
denitrification bacteria, Alcaligenes faecalis strain WT14. Journal
of Environmental Management, 282, 111961.
Chen, L., Chen, L., Pan, D., Lin, H., Ren, Y., Zhang, J. et al. (2021)
Heterotrophic nitrification and related functional gene expression
characteristics of Alcaligenes faecalis SDU20 with the potential
use in swine wastewater treatment. Bioprocess and Biosystems
Engineering, 23, 116.
Daims, H., Lebedeva, E.V., Pjevac, P., Han, P., Herbold, C.,
Albertsen, M. et al. (2015) Complete nitrification by Nitrospira
bacteria. Nature, 528, 504509.
Edayathumangalam, R., Wu, R., Garcia, R., Wang, Y., Wang, W.,
Kreinbring, C. et al. (2013) Crystal structure of Bacillus subtilis
GabR, an autorepressor and transcriptional activator of gabT.
Proceedings of the National Academy of Sciences of the
United States of America, 110, 1782017825.
Frear, D.S. & Burrell, R.C. (1955) Spectrophotometric method for
determining hydroxylamine reductase activity in higher plants.
Analytical Chemistry, 27, 16641665.
Gallegos, M.-T., Schleif, R., Bairoch, A., Hofmann, K. & Ramos, J.
(1997) AraC/XylS family of transcriptional regulators. Microbiol-
ogy and Molecular Biology Reviews, 61, 393410.
Holmes, D.E., Dang, Y. & Smith, J.A. (2019) Nitrogen cycling during
wastewater treatment. Advances in Applied Microbiology, 106,
113192.
Hou, T.-T., Miao, L.-L., Peng, J.-S., Ma, L., Huang, Q., Liu, Y. et al.
(2022) Dirammox is widely distributed and dependently involved
in Alcaligenes and is important to nitrogen cycle. Frontiers in
Microbiology, 13, 864063.
Huang, Y., An, Q., Zhao, B., Lv, Q. & Guo, J. (2018) Potential for aer-
obic NO
2
reduction and corresponding key enzyme genes
involved in Alcaligenes faecalis strain NR. Archives of Microbiol-
ogy, 200, 147158.
Kartal, B., Maalcke, W.J., de Almeida, N.M., Cirpus, I., Gloerich, J.,
Geerts, W. et al. (2011) Molecular mechanism of anaerobic
ammonium oxidation. Nature, 479, 127130.
Ke, Z., Zhou, Y., Jiang, W., Zhang, M., Wang, H., Ren, Y. et al.
(2021) McbG, a LysR family transcriptional regulator activates
the mcbBCDEF gene cluster involved in the upstream pathway
of carbaryl degradation in pseudomonas sp. XWY-1. Applied
and Environmental Microbiology, 87, e02970e02920.
Kessel, M.V., Speth, D.R., Albertsen, M., Nielsen, P.H., Op, D.,
Kartal, B. et al. (2015) Complete nitrification by a single microor-
ganism. Nature, 528, 555571.
Klucar, L., Stano, M. & Hajduk, M. (2009) PhiSITE: database of gene
regulation in bacteriophages. Nucleic Acids Research, 38,
366370.
Kuenen, J.G. (2008) Anammox bacteria: from discovery to applica-
tion. Nature Reviews. Microbiology, 6, 320326.
Kuypers, M., Marchant, H. & Kartal, B. (2018) The microbial nitrogen-
cycling network. Nature Reviews. Microbiology, 16, 263267.
Liu, Y., Wang, Y., Li, Y., An, H. & Lv, Y. (2015) Nitrogen removal char-
acteristics of heterotrophic nitrification-aerobic denitrification by
Alcaligenes faecalis C16. Chemical Engineering Journal, 23,
827834.
Maddocks, S.E. & Oyston, P.C.F. (2008) Structure and function of the
LysR-type transcriptional regulator (LTTR) family proteins.
Microbiology, 154, 36093623.
Molina-Henares, J.A., Krell, T., Guazzaroni, M.E., Segura, A. &
Ramos, J.L. (2005) Members of the IclR family of bacterial tran-
scriptional regulators function as activators and/or repressors.
FEMS Microbiology Reviews, 30, 157186.
Mu, Y., Xu, S., Liu, G., Cheng, M., Dai, W., Chen, Q. et al. (2022) The
novel monooxygenase gene dipD in the dip gene cluster of Alca-
ligenes faecalis JQ135 is essential for the initial catabolism of
dipicolinic acid. Applied and Environmental Microbiology, 88,
e0036022.
Neerackal, G.M., Ndegwa, P.M., Joo, H.S., Wang, X., Frear, C.S.,
Harrison, J.H. et al. (2016) Potential application of Alcaligenes
faecalis strain No. 4 in mitigating ammonia emissions from dairy
wastewater. Bioresource Technology, 206, 3642.
Okuda, K., Kato, S., Ito, T., Shiraki, S., Kawase, Y., Goto, M. et al.
(2014) Role of the aminotransferase domain in Bacillus subtilis
GabR, a pyridoxal 50-phosphate-dependent transcriptional regu-
lator. Molecular Microbiology, 95, 245257.
Papen, H., von Berg, R., Hinkel, I., Thoene, B. & Rennenberg, H.
(1989) Heterotrophic nitrification by Alcaligenes faecalis:NO
2
,
NO
3
,N
2
O, and NO production in exponentially growing cul-
tures. Applied and Environmental Microbiology, 55, 20682072.
Qaidi, S., Yang, J., Zhang, J.-R., Metzger, D. & Bai, G. (2013) The
vitamin B6 biosynthesis pathway in Streptococcus pneumoniae
is controlled by pyridoxal 50-phosphate and the transcription fac-
tor PdxR and has an impact on ear infection. Journal of Bacteri-
ology, 195, 21872196.
Qiu, J., Liu, B., Zhao, L., Zhang, Y., Dan, C., Xin, Y. et al. (2018) A
novel degradation mechanism for pyridine derivatives in Alcali-
genes faecalis JQ135. Applied and Environmental Microbiology,
84, 51085114.
Ramos, J.L., Martínez-Bueno, M., Molina-Henares, A.J., Ter
an, W.,
Watanabe, K., Zhang, X. et al. (2005) The TetR family of tran-
scriptional repressors. Microbiology and Molecular Biology
Reviews, 2, 326356.
Reese, M. (2002) Application of a time-delay neural network to pro-
moter annotation in the drosophila melanogaster genome. Com-
puters & Chemistry, 26, 5156.
Rigali, S., Derouaux, A., Giannotta, F. & Dusart, J. (2002) Subdivision
of the helix-turn-helix GntR family of bacterial regulators in the
FadR, HutC, MocR, and YtrA subfamilies. The Journal of Biolog-
ical Chemistry, 277, 1250712515.
Sambrock, J. & Russel, D.W. (2001) Molecular cloning: a laboratory
manual. New York: Cold Spring Harbor Laboratory Press.
Schleif, R. (2010) AraC protein, regulation of the L-arabinose operon
in Escherichia coli, and the light switch mechanism of AraC
action. FEMS Microbiology Reviews, 34, 779796.
Shoda, M. (2017) Heterotrophic nitrification and aerobic denitrification
by Alcaligenes faecalis No. 4. Journal of Bioscience and Bioen-
gineering, 117, 737741.
Silva, S., Echeverrigaray, S. & Gerhardt, G. (2011) BacPP: bacterial
promoter prediction-a tool for accurate sigma-factor specific
assignment in enterobacteria. Journal of Theoretical Biology,
287, 9299.
Song, T., Zhang, X., Li, J., Wu, X. & Dong, W. (2021) A review of
research progress of heterotrophic nitrification and aerobic deni-
trification microorganisms (HNADMs). Science of the Total Envi-
ronment, 801, 149319.
Stein, L. (2011) Heterotrophic nitrification and nitrifier denitrification.
Nitrification (pp. 95114). Washington, DC: ASM Press.
Taw, M., Lee, H.-I., Lee, S.-H. & Chang, W.-S. (2015) Characteriza-
tion of MocR, a GntR-like transcriptional regulator, in Bradyrhizo-
bium japonicum: its impact on motility, biofilm formation, and
soybean nodulation. Journal of Microbiology, 53, 518525.
MocR FAMILY TRANSCRIPTIONAL REGULATOR DnfR HAS MULTIPLE BINDING 13
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Tramonti, A., Fiascarelli, A., Milano, T., Salvo, M., Nogués, I.,
Pascarella, S. et al. (2015) Molecular mechanism of PdxRa
transcriptional activator involved in the regulation of vitamin B6
biosynthesis in the probiotic bacterium Bacillus clausii.The
FEBS Journal, 282, 29662984.
Tramonti, A., Milano, T., Nardella, C., di Salvo, M., Pascarella, S. &
Contestabile, R. (2016) Salmonella typhimurium PtsJ is a novel
MocR-like transcriptional repressor involved in regulating the
vitamin B6 salvage pathway. The FEBS Journal, 284, 466484.
Tramonti, A., Nardella, C., di Salvo, M., Pascarella, S. &
Contestabile, R. (2018) The MocR-like transcription factors: pyri-
doxal 50-phosphate-dependent regulators of bacterial metabo-
lism. The FEBS Journal, 285, 39253945.
Wang, Q., Lu, X., Yang, H., Yan, H. & Wen, Y. (2021) Redox-sensitive
transcriptional regulator SoxR directly controls antibiotic produc-
tion, development and thiol-oxidative stress response in Strepto-
myces avermitilis.Microbial Biotechnology, 15, 561576.
Wiethaus, J., Schubert, B., Pfänder, Y., Narberhaus, F. &
Masepohl, B. (2008) The GntR-like regulator TauR activates
expression of taurine utilization genes in Rhodobacter capsula-
tus.Journal of Bacteriology, 190, 487493.
Wu, M.R., Hou, T.T., Liu, Y., Miao, L.L., Ai, G.M., Ma, L. et al. (2021)
Novel Alcaligenes ammonioxydans sp. nov. from wastewater
treatment sludge oxidizes ammonia to N
2
with a previously
unknown pathway. Environmental Microbiology, 23, 69656980.
Wu, M.-R., Miao, L.-L., Liu, Y., Qian, X.-X., Hou, T.-T., Ai, G.-M. et al.
(2022) Identification and characterization of a novel hydroxyl-
amine oxidase, DnfA, that catalyzes the oxidation of hydroxyl-
amine to N
2
.The Journal of Biological Chemistry, 298, 102372.
Wu, R., Sanishvili, R., Belitsky, B., Juncosa, J., Le, H., Lehrer, H.
et al. (2017) PLP and GABA trigger GabR-mediated transcrip-
tion regulation in Bacillus subtilis via external aldimine formation.
Proceedings of the National Academy of Sciences of the
United States of America, 114, 38913896.
Xu, S., Qian, X., Jiang, Y., Qin, Y., Zhang, F., Zhang, K. et al. (2022)
Genetic foundations of direct ammonia oxidation (Dirammox) to
N
2
and MocR-like transcriptional regulator DnfR in Alcaligenes
faecalis strain JQ135. Applied and Environmental Microbiology,
88, e0226121.
Xu, S., Wang, X., Zhang, F., Jiang, Y., Zhang, Y., Cheng, M. et al.
(2022) PicR as a MarR family transcriptional repressor multiply
controls the transcription of picolinic acid degradation gene clus-
ter pic in Alcaligenes faecalis JQ135. Applied and Environmental
Microbiology, 88, 0017200122.
Yu, Q., Cai, H., Zhang, Y., Yongzhi, H., Chen, L., Merritt, J. et al.
(2016) Negative regulation of ectoine uptake and catabolism in
Sinorhizobium meliloti: characterization of the ehuR gene. Jour-
nal of Bacteriology, 199, JB.00119-00116.
Zhang, Y., Chen, Q., Ji, J., Zhao, L., Zhang, L., Qiu, J. et al. (2018)
Complete genome sequence of Alcaligenes faecalis strain
JQ135, a bacterium capable of efficiently degrading nicotinic
acid. Current Microbiology, 12, 15511554.
SUPPORTING INFORMATION
Additional supporting information can be found online
in the Supporting Information section at the end of this
article.
How to cite this article: Xu, S.-Q., Wang, X.,
Xu, L., Wang, K.-X., Jiang, Y.-H., Zhang, F.-Y.
et al. (2022) The MocR family transcriptional
regulator DnfR has multiple binding sites and
regulates Dirammox gene transcription in
Alcaligenes faecalis JQ135. Environmental
Microbiology,114. Available from: https://doi.
org/10.1111/1462-2920.16318
14 XU ET AL.
14622920, 0, Downloaded from https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16318 by Nanjing Agricultural, Wiley Online Library on [23/12/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
... faecalis JQ135 possess the ability of Dirammox. The dnfABC cluster in A. faecalis JQ135 contains key genes involving in the Dirammox process with DnfR serving as the positive transcriptional regulator (Xu, Qian, et al., 2022;Xu, Wang, et al., 2022). However, considering the huge taxonomic difference in Dirammox activity, further exploring into the function and molecular mechanisms of the dnf gene cluster in other Alcaligenes species like A. ammonioxydans HO-1 in vivo is highly desired. ...
... Moreover, recent studies have further refined the organization of dnf cluster in A. faecalis JQ135, including dnfABC and dnfDEFGHIR genes (Xu, Qian, et al., 2022). Gene clusters regulated by DnfR and dnfDEGI genes were predicted to be involved in nitrogen-related metabolism (Xu, Wang, et al., 2022). For example, DnfH is predicted to be a phosphoserine aminotransferase, while both DnfI and DnfG have been described as serine hydroxymethyltransferase. ...
Article
Full-text available
Bacteria capable of direct ammonia oxidation (Dirammox) play important roles in global nitrogen cycling and nutrient removal from wastewater. Dirammox process, NH3 → NH2OH → N2, first defined in Alcaligenes ammonioxydans HO‐1 and encoded by dnf gene cluster, has been found to widely exist in aquatic environments. However, because of multidrug resistance in Alcaligenes species, the key genes involved in the Dirammox pathway and the interaction between Dirammox process and the physiological state of Alcaligenes species remain unclear. In this work, ammonia removal via the redistribution of nitrogen between Dirammox and microbial growth in A. ammonioxydans HO‐1, a model organism of Alcaligenes species, was investigated. The dnfA, dnfB, dnfC, and dnfR genes were found to play important roles in the Dirammox process in A. ammonioxydans HO‐1, while dnfH, dnfG, and dnfD were not essential genes. Furthermore, an unexpected redistribution phenomenon for nitrogen between Dirammox and cell growth for ammonia removal in HO‐1 was revealed. After the disruption of the Dirammox in HO‐1, more consumed NH4⁺ was recovered as biomass‐N via rapid metabolic response and upregulated expression of genes associated with ammonia transport and assimilation, tricarboxylic acid cycle, sulfur metabolism, ribosome synthesis, and other molecular functions. These findings deepen our understanding of the molecular mechanisms for Dirammox process in the genus Alcaligenes and provide useful information about the application of Alcaligenes species for ammonia‐rich wastewater treatment.
Article
Full-text available
Nitrogen gas in the atmosphere is partially replenished by microbial denitrification of ammonia. Recent study has shown Alcaligenes ammonioxydans oxidizes ammonia to dinitrogen via a process featuring the intermediate hydroxylamine, termed “Dirammox” (direct ammonia oxidation). However, the unique biochemistry of this process remains unknown. Here we report an enzyme involved in Dirammox that catalyzes the conversion of hydroxylamine to N2. We tested previously annotated proteins involved in redox reactions, DnfA, DnfB, and DnfC, to determine their ability to catalyze the oxidation of ammonia or hydroxylamine. Our results showed that none of these proteins bound to ammonia or catalyzed its oxidation; however, we did find DnfA bound to hydroxylamine. Further experiments demonstrated, in the presence of NADH and FAD, DnfA catalyzed the conversion of ¹⁵N-labeled hydroxylamine to ¹⁵N2. This conversion did not happen under O2-free conditions, and the involvement of oxygen was further confirmed using radiolabeled ¹⁸O2. Thus, we concluded DnfA encodes a hydroxylamine oxidase. We demonstrate DnfA is not homologous to any known hydroxylamine oxidoreductases and contains a diiron center, which was shown to be involved in catalysis via electron paramagnetic resonance experiments. Furthermore, enzyme kinetics of DnfA were assayed, revealing a Km of 92.9 ± 3.0 μM for hydroxylamine and a kcat of 0.028 ± 0.001 s⁻¹. Finally, we show DnfA was localized in the cytoplasm and periplasm, as well as in tubular membrane invaginations in HO-1 cells. To the best of our knowledge, we conclude DnfA is the first enzyme discovered that catalyzes oxidation of hydroxylamine to N2.
Article
Full-text available
Dipicolinic acid (DPA), an essential pyridine derivative biosynthesized in Bacillus spores, constitutes a major proportion of global biomass carbon pool. Alcaligenes faecalis strain JQ135 could catabolize DPA through the "3HDPA (3-hydroxydipicolinic acid) pathway." However, the genes involved in this 3HDPA pathway are still unknown. In this study, a dip gene cluster responsible for DPA degradation was cloned from strain JQ135. The expression of dip genes was induced by DPA and negatively regulated by DipR. A novel monooxygenase gene, dipD, was crucial for the initial hydroxylation of DPA into 3HDPA and proposed to encode the key catalytic component of the multicomponent DPA monooxygenase. The heme binding protein gene dipF, ferredoxin reductase gene dipG, and ferredoxin genes dipJ/dipK/dipL were also involved in the DPA hydroxylation and proposed to encode other components of the multicomponent DPA monooxygenase. The 18O2 stable isotope labeling experiments confirmed that the oxygen atom in the hydroxyl group of 3HDPA came from dioxygen molecule rather than water. The protein sequence of DipD exhibits no significant sequence similarities with known oxygenases, suggesting that DipD was a new member of oxygenase family. Moreover, bioinformatic survey suggested that the dip gene cluster was widely distributed in many Alpha-, Beta-, and Gammaproteobacteria, including soil bacteria, aquatic bacteria, and pathogens. This study provides new molecular insights into the catabolism of DPA in bacteria. IMPORTANCE Dipicolinic acid (DPA) is a natural pyridine derivative that serves as an essential component of the Bacillus spore. DPA accounts for 5 to 15% of the dry weight of spores. Due to the huge number of spores in the environment, DPA is also considered to be an important component of the global biomass carbon pool. DPA could be decomposed by microorganisms and enter the global carbon cycling; however, the underlying molecular mechanisms are rarely studied. In this study, a DPA catabolic gene cluster (dip) was cloned and found to be widespread in Alpha-, Beta-, and Gammaproteobacteria. The genes responsible for the initial hydroxylation of DPA to 3-hydroxyl-dipicolinic acid were investigated in Alcaligenes faecalis strain JQ135. The present study opens a door to elucidate the mechanism of DPA degradation and its possible role in DPA-based carbon biotransformation on earth.
Article
Full-text available
The pic gene cluster was found to be responsible for PA degradation and widely distributed in Alpha- , Beta- , and Gammaproteobacteria . Thus, it is very necessary to understand the regulation mechanism of the pic cluster in these strains.
Article
Full-text available
Nitrogen cycle is an essential process for environmental health. Dirammox ( dir ect amm onia ox idation), encoded by the dnfT1RT2ABCD cluster, was a novel pathway for microbial N 2 production defined in Alcaligenes ammonioxydans HO-1. Here, a copy of the cluster dnfT1RT2ABCD as a whole was proved to have existed and very conserved in all Alcaligenes genomes. Phylogenetic analyses based on 16S rRNA gene sequences and amino acid sequences of DnfAs, together with G + C content data, revealed that dnf cluster was evolved associated with the members of the genus Alcaligenes . Under 20% O 2 conditions, 14 of 16 Alcaligenes strains showed Dirammox activity, which seemed likely taxon-related. However, the in vitro activities of DnfAs catalyzing the direct oxidation of hydroxylamine to N 2 were not taxon-related but depended on the contents of Fe and Mn ions. The results indicated that DnfA is necessary but not sufficient for Dirammox activity. The fact that members of the genus Alcaligenes are widely distributed in various environments, including soil, water bodies (both freshwater and seawater), sediments, activated sludge, and animal–plant-associated environments, strongly suggests that Dirammox is important to the nitrogen cycle. In addition, Alcaligenes species are also commonly found in wastewater treatment plants, suggesting that they might be valuable resources for wastewater treatment.
Article
Full-text available
Ammonia oxidation is an important process in both the natural nitrogen cycle and nitrogen removal from engineered ecosystems. Recently, a new ammonia oxidation pathway termed Dirammox (direct ammonia oxidation, NH3 !NH2OH!N2) has been identified in Alcaligenes ammonioxydans. However, whether Dirammox is present in other microbes, as well as its genetic regulation, remains unknown. In this study, it was found that the metabolically versatile bacterium Alcaligenes faecalis strain JQ135 could efficiently convert ammonia into N2 via NH2OH under aerobic conditions. Genetic deletion and complementation results suggest that dnfABC is responsible for the ammonia oxidation to N2 in this strain. Strain JQ135 also employs aerobic denitrification, mainly producing N2O and trace amounts of N2, with nitrite as the sole nitrogen source. Deletion of the nirK and nosZ genes, which are essential for denitrification, did not impair the capability of JQ135 to oxidize ammonia to N2 (i.e., Dirammox is independent of denitrification). Furthermore, it was also demonstrated that pod (which encodes pyruvic oxime dioxygenase) was not involved in Dirammox and that AFA_16745 (which was previously annotated as ammonia monooxygenase and is widespread in heterotrophic bacteria) was not an ammonia monooxygenase. The MocR-family transcriptional regulator DnfR was characterized as an activator of the dnfABC operon with the binding motif 59-TGGTCTGT-39 in the promoter region. A bioinformatic survey showed that homologs of dnf genes are widely distributed in heterotrophic bacteria. In conclusion, this work demonstrates that, besides A. ammonioxydans, Dirammox occurs in other bacteria and is regulated by the MocR-family transcriptional regulator DnfR.
Article
Full-text available
The tetracycline repressor (TetR) belongs to the most popular, versatile and efficient transcriptional regulators used in bacterial genetics. In the tetracycline (Tc) resistance determinant tet(B) of transposon Tn10, tetR regulates the expression of a divergently oriented tetA gene that encodes a Tc antiporter. These components of Tn10 and of other natural or synthetic origins have been used for tetracycline‐dependent gene regulation (tet regulation) in at least 40 bacterial genera. Tet regulation serves several purposes such as conditional complementation, depletion of essential genes, modulation of artificial genetic networks, protein overexpression or the control of gene expression within cell culture or animal infection models. Adaptations of the promoters employed have increased tet regulation efficiency and have made this system accessible to taxonomically distant bacteria. Variations of TetR, different effector molecules and mutated DNA binding sites have enabled new modes of gene expression control. This article provides a current overview of tet regulation in bacteria.
Article
Full-text available
A new heterotrophic nitrifying bacterium was isolated from the compost of swine manure and rice husk and identified as Alcaligenes faecalis SDU20. Strain SDU20 had heterotrophic nitrification potential and could remove 99.7% of the initial NH4⁺–N. Nitrogen balance analysis revealed that 15.9 and 12.3% of the NH4⁺–N were converted into biological nitrogen and nitrate nitrogen, respectively. The remaining 71.44% could be converted into N2 or N2O. Single-factor experiments showed that the optimal conditions for ammonium removal were the carbon source of sodium succinate, C/N ratio 10, initial pH 8.0, and temperature 30 °C. Nitrification genes were determined to be upregulated when sodium succinate was used as the carbon source analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Strain SDU20 could tolerate 4% salinity and show resistance to some heavy metal ions. Strain SDU20 removed 72.6% high concentrated NH4⁺–N of 2000 mg/L within 216 h. In a batch experiment, the highest NH4⁺–N removal efficiency of 98.7% and COD removal efficiency of 93.7% were obtained in the treatment of unsterilized swine wastewater. Strain SDU20 is promising in high-ammonium wastewater treatment.
Article
Heterotrophic nitrifiers are able to oxidize and remove ammonia from nitrogen‐rich wastewaters but the genetic elements of heterotrophic ammonia oxidation are poorly understood. Here, we isolated and identified a novel heterotrophic nitrifier, Alcaligenes ammonioxydans sp. nov. strain HO‐1, oxidizing ammonia to hydroxylamine and ending in the production of N2 gas. Genome analysis revealed that strain HO‐1 encoded a complete denitrification pathway but lacks any genes coding for homologous to known ammonia monooxygenases or hydroxylamine oxidoreductases. Our results demonstrated strain HO‐1 denitrified nitrite (not nitrate) to N2 and N2O at anaerobic and aerobic conditions respectively. Further experiments demonstrated that inhibition of aerobic denitrification did not stop ammonia oxidation and N2 production. A gene cluster (dnfT1RT2ABCD) was cloned from strain HO‐1 and enabled E. coli accumulated hydroxylamine. Sub‐cloning showed that genetic cluster dnfAB or dnfABC already enabled E. coli cells to produce hydroxylamine and further to 15N2 from (15NH4)2SO4. Transcriptome analysis revealed these three genes dnfA, dnfB and dnfC were significantly upregulated in response to ammonia stimulation. Taken together, we concluded that strain HO‐1 has a novel dnf genetic cluster for ammonia oxidation and this dnf genetic cluster encoded a previously unknown pathway of direct ammonia oxidation (Dirammox) to N2.
Article
Traditional nitrogen removal relies on the autotrophic nitrification and anaerobic denitrification process. In the system, autotrophic microorganisms achieve nitrification under aerobic condition and heterotrophic microorganisms complete the denitrification in anaerobic condition. As the two types of microorganisms have different tolerance on oxygen concentration, nitrification and denitrification are normally set in two compartments for high nitrogen removal. Therefore, large land occupying is required. In fact, there is a special type of microorganism called heterotrophic nitrification & aerobic denitrification microorganisms (HNADMs) which can oxidize ammonium nitrogen, and perform denitrification in the presence of oxygen. HNADMs have been reported in many environments. It was found that HNADMs could simultaneously achieve nitrification and denitrification. In addition, some HNADMs not only have the ability to remove nitrogen, but also have the ability to remove phosphorus. It suggests that HNADMs have great potential for pollution removal from wastewater. So far, individual work on single strain was carried out. Comprehensive summary of the HNADMs would provide a better picture for understanding and directing its application. In this paper, the studies related on HNADMs were reviewed. The nitrogen metabolism pathway of HNADMs was summarized. The impact of pH, DO, carbon source, and C/N on HNADMs growth and metabolism were discussed. In addition, the extracellular polymeric substance (EPS) production, quorum sensing (QS) secretion and P removal by HNADMs were displayed.
Article
The ArC/XylS family of prokaryotic positive transcriptional regulators includes more than 100 proteins and polypeptides derived from open reading frames translated from DNA sequences. Members of this family are widely distributed and have been found in the gamma subgroup of the proteobacteria, low- and high-G + C-content gram-positive bacteria, and cyanobacteria. These proteins are defined by a profile that can be accessed from PROSITE PS01124. Members of the family are about 300 amino acids long and have three main regulatory functions in common: carbon metabolism, stress response, and pathogenesis. Multiple alignments of the proteins of the family define a conserved stretch of 99 amino acids usually located at the C-terminal region of the regulator and connected to a nonconserved region via a linker. The conserved stretch contains all the elements required to bind DNA target sequences and to activate transcription from cognate promoters. Secondary analysis of the conserved region suggests that it contains two potential alpha-helix-turn-alpha-helix DNA binding motifs. The first, and better-fitting motif is supported by biochemical data, whereas existing biochemical data neither support nor refute the proposal that the second region possesses this structure. The phylogenetic relationship suggests that members of the family have recruited the nonconserved domain(s) into a series of existing domains involved in DNA recognition and transcription stimulation and that this recruited domain governs the role that the regulator carries out. For some regulators, it has been demonstrated that the nonconserved region contains the dimerization domain. For the regulators involved in carbon metabolism, the effector binding determinants are also in this region. Most regulators belonging to the AraC/XylS family recognize multiple binding sites in the regulated promoters. One of the motifs usually overlaps or is adjacent to the -35 region of the cognate promoters. Footprinting assays have suggested that these regulators protect a stretch of up to 20 bp in the target promoters, and multiple alignments of binding sites for a number of regulators have shown that the proteins recognize short motifs within the protected region.