bluuebunny/crossref_metadata_2025_split huggingface dataset:
The
hetC
Gene Is a Direct Target of the NtcA Transcriptional Regulator in Cyanobacterial Heterocyst Development
Authors: Muro-Pastor Alicia M. , Valladares Ana , Flores Enrique , Herrero Antonia 
Published: December 2019

ABSTRACT

The heterocyst is the site of nitrogen fixation in aerobically grown cultures of some filamentous cyanobacteria. Heterocyst development in
Anabaena
sp. strain PCC 7120 is dependent on the global nitrogen regulator NtcA and requires, among others, the products of the
hetR
and
hetC
genes. Expression of
hetC
, tested by RNA- DNA hybridization, was impaired in an
ntcA
mutant. A nitrogen-regulated, NtcA-dependent putative transcription start point was localized at nucleotide −571 with respect to the
hetC
translational start. Sequences upstream from this transcription start point exhibit the structure of the canonical cyanobacterial promoter activated by NtcA, and purified NtcA protein specifically bound to a DNA fragment containing this promoter. Activation of expression of
hetC
during heterocyst development appears thus to be directly operated by NtcA. NtcA-mediated activation of
hetR
expression was not impaired in a
hetC
mutant, indicating that HetC is not an NtcA-dependent element required for
hetR
induction.
Evidence of Horizontal Transfer of the
Eco
O109I Restriction-Modification Gene to
Escherichia coli
Chromosomal DNA
Authors: Kita Keiko , Tsuda Junko , Kato Toshinobu , Okamoto Kenji , Yanase Hideshi , Tanaka Masashi 
Published: December 2019

ABSTRACT

A DNA fragment carrying the genes coding for
Eco
O109I endonuclease and
Eco
O109I methylase, which recognize the nucleotide sequence 5′-(A/G)GGNCC(C/T)-3′, was cloned from the chromosomal DNA of
Escherichia coli
H709c. The
Eco
O109I restriction-modification (R-M) system was found to be inserted between the
int
and
psu
genes from satellite bacteriophage P4, which were lysogenized in the chromosome at the P4 phage attachment site of the corresponding
leuX
gene observed in
E. coli
K-12 chromosomal DNA. The
sid
gene of the prophage was inactivated by insertion of one copy of IS
21
. These findings may shed light on the horizontal transfer and stable maintenance of the R-M system.
Expression of the
Escherichia coli
Ada Regulon in Stationary Phase: Evidence for
rpoS
-Dependent Negative Regulation of
alkA
Transcription
Authors: Landini Paolo , Busby Stephen J. W. 
Published: December 2019

ABSTRACT

The
Escherichia coli
Ada protein activates ς
70
-dependent transcription at three different promoters (
ada
,
aidB
, and
alkA
) in response to alkylation damage of DNA. During stationary phase, however, the methylated form of Ada shuts off expression of
alkA
; this repression is specific for ς
S
-dependent transcription. Thus, at the
alkA
promoter, the Ada protein can act as both a positive and negative modulator of the adaptive response to alkylation damage, depending on the cell’s physiological state.
TheAgrobacterium tumefaciensChaperone-Like Protein, VirE1, Interacts with VirE2 at Domains Required for Single-Stranded DNA Binding and Cooperative Interaction
Authors: Sundberg Christopher D. , Ream Walt 
Published: December 2019

ABSTRACTAgrobacterium tumefacienstransfers single-stranded DNA (ssDNA) into plants. Efficient tumorigenesis requires VirE1-dependent export of ssDNA-binding (SSB) protein VirE2. VirE1 binds VirE2 domains involved in SSB and self-association, and VirE1 may facilitate VirE2 export by preventing VirE2 aggregation and the premature binding of VirE2 to ssDNA.
Partition of the Linear Plasmid N15: Interactions of N15 Partition Functions with the
sop
Locus of the F Plasmid
Authors: Ravin N. , Lane D. 
Published: December 2019

ABSTRACT

A locus close to one end of the linear N15 prophage closely resembles the
sop
operon which governs partition of the F plasmid; the promoter region contains similar operator sites, and the two putative gene products have extensive amino acid identity with the SopA and -B proteins of F. Our aim was to ascertain whether the N15
sop
homologue functions in partition, to identify the centromere site, and to examine possible interchangeability of function with the F Sop system. When expressed at a moderate level, N15 SopA and -B proteins partly stabilize mini-F which lacks its own
sop
operon but retains the
sopC
centromere. The stabilization does not depend on increased copy number. Likewise, an N15 mutant with most of its
sop
operon deleted is partly stabilized by F Sop proteins and fully stabilized by its own. Four inverted repeat sequences similar to those of
sopC
were located in N15. They are distant from the
sop
operon and from each other. Two of these were shown to stabilize a mini-F
sop
deletion mutant when N15 Sop proteins were provided. Provision of the SopA homologue to plasmids with a
sopA
deletion resulted in further destabilization of the plasmid. The N15 Sop proteins exert effective, but incomplete, repression at the F
sop
promoter. We conclude that the N15
sop
locus determines stable inheritance of the prophage by using dispersed centromere sites. The SopB-centromere and SopA-operator interactions show partial functional overlap between N15 and F. SopA of each plasmid appears to interact with SopB of the other, but in a way that is detrimental to plasmid maintenance.
The Bacteriophage P1 HumD Protein Is a Functional Homolog of the Prokaryotic UmuD′-Like Proteins and Facilitates SOS Mutagenesis in
Escherichia coli
Authors: McLenigan Mary P. , Kulaeva Olga I. , Ennis Don G. , Levine Arthur S. , Woodgate Roger 
Published: December 2019

ABSTRACT

The
Escherichia coli umuD
and
umuC
genes comprise an operon and encode proteins that are involved in the mutagenic bypass of normally replication-inhibiting DNA lesions. UmuD is, however, unable to function in this process until it undergoes a RecA-mediated cleavage reaction to generate UmuD′. Many homologs of
umuDC
have now been identified. Most are located on bacterial chromosomes or on broad-host-range R plasmids. One such putative homolog,
humD
(homolog of
umuD
) is, however, found on the bacteriophage P1 genome. Interestingly,
humD
differs from other
umuD
homologs in that it encodes a protein similar in size to the posttranslationally generated UmuD′ protein and not UmuD, nor is it in an operon with a cognate
umuC
partner. To determine if HumD is, in fact, a bona fide homolog of the prokaryotic UmuD′-like mutagenesis proteins, we have analyzed the ability of HumD to complement UmuD′ functions in vivo as well as examined HumD’s physical properties in vitro. When expressed from a high-copy-number plasmid, HumD restored cellular mutagenesis and increased UV survival to normally nonmutable
recA430 lexA
(Def) and UV-sensitive Δ
umuDC recA718 lexA
(Def) strains, respectively. Complementing activity was reduced when HumD was expressed from a low-copy-number plasmid, but this observation is explained by immunoanalysis which indicates that HumD is normally poorly expressed in vivo. In vitro analysis revealed that like UmuD′, HumD forms a stable dimer in solution and is able to interact with
E. coli
UmuC and RecA nucleoprotein filaments. We conclude, therefore, that bacteriophage P1 HumD is a functional homolog of the UmuD′-like proteins, and we speculate as to the reasons why P1 might require the activity of such a protein in vivo.
Preprotein Translocation by a Hybrid Translocase Composed of
Escherichia coli
and
Bacillus subtilis
Subunits
Authors: Swaving Jelto , van Wely Karel H. M. , Driessen Arnold J. M. 
Published: December 2019

ABSTRACT

Bacterial protein translocation is mediated by translocase, a multisubunit membrane protein complex that consists of a peripheral ATPase SecA and a preprotein-conducting channel with SecY, SecE, and SecG as subunits. Like
Escherichia coli
SecG, the
Bacillus subtilis
homologue, YvaL, dramatically stimulated the ATP-dependent translocation of precursor PhoB (prePhoB) by the
B. subtilis
SecA-SecYE complex. To systematically determine the functional exchangeability of translocase subunits, all of the relevant combinations of the
E. coli
and
B. subtilis secY
,
secE
, and
secG
genes were expressed in
E. coli
. Hybrid SecYEG complexes were overexpressed at high levels. Since SecY could not be overproduced without SecE, these data indicate a stable interaction between the heterologous SecY and SecE subunits.
E. coli
SecA, but not
B. subtilis
SecA, supported efficient ATP-dependent translocation of the
E. coli
precursor OmpA (proOmpA) into inner membrane vesicles containing the hybrid SecYEG complexes, if
E. coli
SecY and either
E. coli
SecE or
E. coli
SecG were present. Translocation of
B. subtilis
prePhoB, on the other hand, showed a strict dependence on the translocase subunit composition and occurred efficiently only with the homologous translocase. In contrast to
E. coli
SecA,
B. subtilis
SecA binds the SecYEG complexes only with low affinity. These results suggest that each translocase subunit contributes in an exclusive manner to the specificity and functionality of the complex.
Two New Early Bacteriophage T4 Genes,
repEA
and
repEB
, That Are Important for DNA Replication Initiated from Origin E
Authors: Vaiskunaite Rita , Miller Andrew , Davenport Laura , Mosig Gisela 
Published: December 2019

ABSTRACT

Two new, small, early bacteriophage T4 genes,
repEA
and
repEB
, located within the origin E (
oriE
) region of T4 DNA replication, affect functioning of this origin. An important and unusual property of the
oriE
region is that it is transcribed at early and late periods after infection, but in opposite directions (from complementary DNA strands). The early transcripts are mRNAs for RepEA and RepEB proteins, and they can serve as primers for leading-strand DNA synthesis. The late transcripts, which are genuine antisense RNAs for the early transcripts, direct synthesis of virion components. Because the T4 genome contains several origins, and because recombination can bypass a primase requirement for retrograde synthesis, neither defects in a single origin nor primase deficiencies are lethal in T4 (Mosig et al., FEMS Microbiol. Rev. 17:83–98, 1995). Therefore,
repEA
and
repEB
were expected and found to be important for T4 DNA replication only when activities of other origins were reduced. To investigate the in vivo roles of the two
repE
genes, we constructed nonsense mutations in each of them and combined them with the
motA
mutation
sip1
that greatly reduces initiation from other origins. As expected, T4 DNA synthesis and progeny production were severely reduced in the double mutants as compared with the single
motA
mutant, but early transcription of
oriE
was reduced neither in the
motA
nor in the
repE
mutants. Moreover, residual DNA replication and growth of the double mutants were different at different temperatures, suggesting different functions for
repEA
and
repEB
. We surmise that the different structures and protein requirements for functioning of the different origins enhance the flexibility of T4 to adapt to varied growth conditions, and we expect that different origins in other organisms with multiorigin chromosomes might differ in structure and function for similar reasons.
Inactivation of the Tricarboxylic Acid Cycle Aconitase Gene from
Streptomyces viridochromogenes
Tü494 Impairs Morphological and Physiological Differentiation
Authors: Schwartz D. , Kaspar S. , Kienzlen G. , Muschko K. , Wohlleben W. 
Published: December 2019

ABSTRACT

The tricarboxylic acid (TCA) cycle aconitase gene
acnA
from
Streptomyces viridochromogenes
Tü494 was cloned and analyzed. AcnA catalyzes the isomerization of citrate to isocitrate in the TCA cycle, as indicated by the ability of
acnA
to complement the aconitase-deficient
Escherichia coli
mutant JRG3259. An
acnA
mutant was unable to develop aerial mycelium and to sporulate, resulting in a bald phenotype. Furthermore, the mutant did not produce the antibiotic phosphinothricin tripeptide, demonstrating that AcnA also affects physiological differentiation.
An Improved Transposon for the Halophilic Archaeon
Haloarcula hispanica
Authors: Woods Wayne G. , Ngui Katrina , Dyall-Smith Michael L. 
Published: December 2019

ABSTRACT

An improved transposon (ThD
73
) for
Haloarcula hispanica
is described. Based on the halobacterial insertion sequence ISH
28
, it showed little target sequence specificity but was biased toward a lower G+C content. Twenty randomly selected ThD
73
mutants were analyzed, and the DNA flanking their insertions revealed several recognizable sequences, including two (unrelated) ISH elements.
Sulfate Transport in
Penicillium chrysogenum
: Cloning and Characterization of the
sutA
and
sutB
Genes
Authors: van de Kamp Mart , Pizzinini Enrica , Vos Arnold , van der Lende Ted R. , Schuurs Theo A. , Newbert Roger W. , Turner Geoffrey , Konings Wil N. , Driessen Arnold J. M. 
Published: December 2019

ABSTRACT

In industrial fermentations,
Penicillium chrysogenum
uses sulfate as the source of sulfur for the biosynthesis of penicillin. By a PCR-based approach, two genes,
sutA
and
sutB
, whose encoded products belong to the SulP superfamily of sulfate permeases were isolated. Transformation of a sulfate uptake-negative
sB3
mutant of
Aspergillus nidulans
with the
sutB
gene completely restored sulfate uptake activity. The
sutA
gene did not complement the
A. nidulans sB3
mutation, even when expressed under control of the
sutB
promoter. Expression of both
sutA
and
sutB
in
P. chrysogenum
is induced by growth under sulfur starvation conditions. However,
sutA
is expressed to a much lower level than is
sutB
. Disruption of
sutB
resulted in a loss of sulfate uptake ability. Overall, the results show that SutB is the major sulfate permease involved in sulfate uptake by
P. chrysogenum
.
Overexpression of a Dominant-Negative Allele of
SEC4
Inhibits Growth and Protein Secretion in
Candida albicans
Authors: Mao Yuxin , Kalb Vernon F. , Wong Brian 
Published: December 2019

ABSTRACT

Candida albicans SEC4
was cloned by complementing the
Saccharomyces cerevisiae sec4-8
mutation, and its deduced protein product (Sec4p) was 63% identical to
S. cerevisiae
Sec4p. One chromosomal
SEC4
allele in
C. albicans
CAI4 was readily disrupted by homologous gene targeting, but efforts to disrupt the second allele yielded no viable null mutants. Although this suggested that
C. albicans SEC4
was essential, it provided no information about this gene’s functions. Therefore, we constructed a mutant
sec4
allele encoding an amino acid substitution (Ser-28→Asn) analogous to the Ser-17→Asn substitution in a
trans
-dominant inhibitor of mammalian Ras protein.
GAL1
-regulated expression plasmids carrying the mutant
sec4
allele (pS28N) had minimal effects in glucose-incubated
C. albicans
transformants, but six of nine transformants tested grew very slowly in galactose. Incubation of pS28N transformants in galactose also inhibited secretion of aspartyl protease (Sap) and caused 90-nm secretory vesicles to accumulate intracellularly, and plasmid curing restored growth and Sap secretion to wild-type levels. These results imply that
C. albicans SEC4
is required for growth and protein secretion and that it functions at a later step in the protein secretion pathway than formation of post-Golgi secretory vesicles. They also demonstrate the feasibility of using inducible dominant-negative alleles to define the functions of essential genes in
C. albicans.
A Periplasmic Location Is Essential for the Role of the ApbE Lipoprotein in Thiamine Synthesis in
Salmonella typhimurium
Authors: Beck Brian J. , Downs Diana M. 
Published: December 2019

ABSTRACT

ApbE is a lipoprotein in
Salmonella typhimurium
, and mutants unable to make this protein have a reduced ability to make thiamine (vitamin B
1
) and require it as a supplement for optimal growth in minimal glucose medium. Polyclonal antibodies specific to ApbE were used to determine that wild-type ApbE is located exclusively in the inner membrane. The periplasmic, monotopic topology of ApbE was determined by using computer-based hydrophobicity plots, LacZ and PhoA gene fusions, and proteinase protection experiments. This extracellular location of ApbE is required for its function, since a cytoplasmic form (ApbE
cyto
) did not allow an
apbE
mutant to grow in the absence of thiamine. A periplasmic form of ApbE (ApbE
peri
) lacking the lipoprotein modification allowed an
apbE
mutant to grow in the absence of thiamine, indicating that soluble ApbE could function in thiamine synthesis and that lipoation and membrane association were not required. Alteration of the amino acid implicated in membrane sorting for other lipoproteins did not result in a relocalization of ApbE to the outer membrane, suggesting that additional sorting determinants exist for ApbE.
Genes of the
sbo-alb
Locus of
Bacillus subtilis
Are Required for Production of the Antilisterial Bacteriocin Subtilosin
Authors: Zheng Guolu , Yan Liang Z. , Vederas John C. , Zuber Peter 
Published: December 2019

ABSTRACT

Bacillus subtilis
JH642 and a wild strain of
B. subtilis
called 22a both produce an antilisterial peptide that can be purified by anion-exchange and gel filtration chromatography. Amino acid analysis confirmed that the substance was the cyclic bacteriocin subtilosin. A mutant defective in production of the substance was isolated from a plasmid gene disruption library. The plasmid insertion conferring the antilisterial-peptide-negative phenotype was located in a seven-gene operon (
alb
, for antilisterial bacteriocin) residing immediately downstream from the
sbo
gene, which encodes the precursor of subtilosin. An insertion mutation in the
sbo
gene also conferred loss of antilisterial activity. Comparison of the presubtilosin and mature subtilosin sequences suggested that certain residues undergo unusual posttranslational modifications unlike those occurring during the synthesis of class I (lantibiotic) or some class II bacteriocins. The putative products of the genes of the operon identified show similarities to peptidases and transport proteins that may function in processing and export. Two
alb
gene products resemble proteins that function in pyrroloquinoline quinone biosynthesis. The use of
lacZ-alb
and
lacZ-sbo
gene fusions, along with primer extension analysis, revealed that the
sbo-alb
genes are transcribed from a major promoter, residing upstream of
sbo
, that is very likely utilized by the ς
A
form of RNA polymerase. The
sbo
and
alb
genes are negatively regulated by the global transition state regulator AbrB and are also under positive autoregulation that is not mediated by the subtilosin peptide but instead requires one or more of the
alb
gene products.
Transcription Regulation of the Colicin K
cka
Gene Reveals Induction of Colicin Synthesis by Differential Responses to Environmental Signals
Authors: Kuhar Irena , Žgur-Bertok Darja 
Published: December 2019

ABSTRACT

Colicin-producing strains occur frequently in natural populations of
Escherichia coli
, and colicinogenicity seems to provide a competitive advantage in the natural habitat. A
cka-lacZ
fusion was used to study the regulation of expression of the colicin K structural gene. Expression is growth phase dependent, with high activity in the late stationary phase. Nutrient depletion induces the expression of
cka
due to an increase in ppGpp. Temperature is a strong signal for
cka
expression, since only basal-level activity was detected at 22°C. Mitomycin C induction demonstrates that
cka
expression is regulated to a lesser extent by the SOS response independently of ppGpp. Increased osmolarity induces a partial increase, while the global regulator integration host factor inhibits expression in the late stationary phase. Induction of
cka
was demonstrated to be independent of the cyclic AMP-Crp complex, carbon source, RpoS, Lrp, H-NS, pH, and short-chain fatty acids. In contrast to colicin E1,
cka
expression is independent of catabolite repression and is partially affected by anaerobiosis only upon SOS induction. These results indicate that while different colicins are expressed in response to some common signals such as nutrient depletion, the expression of individual colicins could be further influenced by specific environmental cues.
Characterization of the
Bradyrhizobium japonicum ftsH
Gene and Its Product
Authors: Narberhaus Franz , Urech Carmen , Hennecke Hauke 
Published: December 2019

ABSTRACT

The
Bradyrhizobium japonicum ftsH
gene was cloned by using a set of widely applicable degenerated oligonucleotides. Western blot experiments indicated that the FtsH protein was produced under standard growth conditions and that it was not heat inducible. Attempts to delete the
ftsH
gene in
B. japonicum
failed, suggesting a pivotal cellular function of this gene. The expression of
B. japonicum ftsH
in an
ftsH
-negative
Escherichia coli
strain significantly enhanced the fitness of this mutant and reduced the steady-state level of ς
32
.
PRR1
, a Homolog of
Aspergillus nidulans palF
, Controls pH-Dependent Gene Expression and Filamentation in
Candida albicans
Authors: Porta Amalia , Ramon Ana M. , Fonzi William A. 
Published: December 2019

ABSTRACT

The pH of the environment has been implicated in controlling the yeast-hypha transition and pathogenesis of
Candida albicans
. Several
C. albicans
genes, including
PHR1
and
PHR2
, are pH dependent in their expression. To investigate the mechanism of pH-dependent expression, we have cloned and characterized
PRR1
(for pH response regulator).
PRR1
is homologous to
palF
, a component of the pH response pathway in
Aspergillus nidulans
. Expression of
PRR1
was itself pH dependent, being maximal at acid pH but reduced severalfold at alkaline pH. In a
prr1
null mutant the alkaline-induced expression of
PHR1
was completely abolished. Conversely, expression of
PHR2
was no longer repressed at alkaline pH. A
prr1
null mutant exhibited no morphological abnormalities at either pH; however, it lost the ability to form hyphae on medium 199 and on 10% serum plates. The ability to filament on serum was not restored by forced expression of
PHR1
, indicating that additional
PRR1
-dependent genes are required for hyphal development. These developmental genes appear to be distinct from those controlled by the developmental regulator
EFG1
, since the
EFG1
-dependent gene
HWP1
was expressed normally in the
prr1
null mutant. We conclude that
PRR1
encodes a component of the pH-dependent response pathway in
C. albicans
and that this pathway regulates the expression of multiple components of hyphal development.
Effect of Environmental pH on Morphological Development of
Candida albicans
Is Mediated via the PacC-Related Transcription Factor Encoded by
PRR2
Authors: Ramon Ana M. , Porta Amalia , Fonzi William A. 
Published: December 2019

ABSTRACT

The ability to respond to ambient pH is critical to the growth and virulence of the fungal pathogen
Candida albicans
. This response entails the differential expression of several genes affecting morphogenesis. To investigate the mechanism of pH-dependent gene expression, the
C. albicans
homolog of
pacC
, designated
PRR2
(for pH response regulator), was identified and cloned.
pacC
encodes a zinc finger-containing transcription factor that mediates pH-dependent gene expression in
Aspergillus nidulans
. Mutants lacking
PRR2
can no longer induce the expression of alkaline-expressed genes or repress acid-expressed genes at alkaline pH. Although the mutation did not affect growth of the cells at acid or alkaline pH, the mutants exhibited medium-conditional defects in filamentation.
PRR2
was itself expressed in a pH-conditional manner, and its induction at alkaline pH was controlled by
PRR1
.
PRR1
is homologous to
palF
, a regulator of
pacC
. Thus,
PRR2
expression is controlled by a pH-dependent feedback loop. The results demonstrate that the pH response pathway of
Aspergillus
is conserved and that this pathway has been adapted to control dimorphism in
C. albicans
.