bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ABC Transporter Plays a Developmental Aggregation Role in
Myxococcus xanthus
Authors: Ward Mandy J. , Mok Kenny C. , Astling David P. , Lew Helen , Zusman David R. 
Published: December 2019

ABSTRACT

Myxococcus xanthus
is a gram-negative bacterium which has a complex life cycle. Autochemotaxis, a process whereby cells release a self-generated signaling molecule, may be the principal mechanism facilitating directed motility in both the vegetative swarming and developmental aggregation stages of this life cycle. The process requires the Frz signal transduction system, including FrzZ, a protein which is composed of two domains, both showing homology to the enteric chemotaxis response regulator CheY. The first domain of FrzZ (FrzZ1), when expressed as bait in the yeast two-hybrid system and screened against a library, was shown to potentially interact with the C-terminal portion of a protein encoding an ATP-binding cassette (AbcA). The activation domain-AbcA fusion protein did not interact with the second domain of FrzZ (FrzZ2) or with two other
M. xanthus
response regulator-containing proteins presented as bait, suggesting that the FrzZ1-AbcA interaction may be specific. Cloning and sequencing of the upstream region of the
abcA
gene showed the ATP-binding cassette to be linked to a large hydrophobic, potentially membrane-spanning domain. This domain organization is characteristic of a subgroup of ABC transporters which perform export functions. Cloning and sequencing downstream of
abcA
indicated that the ABC transporter is at the start of an operon containing three open reading frames. An insertion mutation in the
abcA
gene resulted in cells displaying the frizzy aggregation phenotype, providing additional evidence that FrzZ and AbcA may be part of the same signal transduction pathway. Cells with mutations in genes downstream of
abcA
showed no developmental defects. Analysis of the proposed exporter role of AbcA in cell mixing experiments showed that the ABC transporter mutant could be rescued by extracellular complementation. We speculate that the AbcA protein may be involved in the export of a molecule required for the autochemotactic process.
The Highly Conserved, Coregulated
SNO
and
SNZ
Gene Families in
Saccharomyces cerevisiae
Respond to Nutrient Limitation
Authors: Padilla Pamela A. , Fuge Edwina K. , Crawford Matthew E. , Errett Allison , Werner-Washburne Margaret 
Published: December 2019

ABSTRACT

SNZ1
, a member of a highly conserved gene family, was first identified through studies of proteins synthesized in stationary-phase yeast cells. There are three
SNZ
genes in
Saccharomyces cerevisiae
, each of which has another highly conserved gene, named
SNO
(
SNZ
proximal open reading frame), upstream. The DNA sequences and relative positions of
SNZ
and
SNO
genes have been phylogenetically conserved. This report details studies of the expression of the
SNZ-SNO
gene pairs under various conditions and phenotypic analysis of
snz-sno
mutants. An analysis of total RNA was used to determine that adjacent
SNZ-SNO
gene pairs are coregulated.
SNZ2/3
and
SNO2/3
mRNAs are induced prior to the diauxic shift and decrease in abundance during the postdiauxic phase, when
SNZ1
and
SNO1
are induced. In
snz2 snz3
mutants,
SNZ1
mRNA is induced prior to the diauxic shift, when
SNZ2/3
mRNAs are normally induced. Under nitrogen-limiting conditions,
SNZ1
mRNAs accumulate in tryptophan, adenine, and uracil auxotrophs but not in prototrophic strains, indicating that induction occurs in response to the limitation of specific nutrients. Strains carrying deletions in all
SNZ-SNO
gene pairs are viable, but
snz1
and
sno1
mutants are sensitive to 6-azauracil (6-AU), an inhibitor of purine and pyrimidine biosynthetic enzymes, and methylene blue, a producer of singlet oxygen. The conservation of sequence and chromosomal position, the coregulation and pattern of expression of
SNZ1
and
SNO1
genes, and the sensitivity of
snz1
and
sno1
mutants to 6-AU support the hypothesis that the associated proteins are part of an ancient response to nutrient limitation.
The SecA Subunit of
Escherichia coli
Preprotein Translocase Is Exposed to the Periplasm
Authors: Eichler Jerry , Wickner William 
Published: December 2019

ABSTRACT
SecA undergoes conformational changes during translocation, inserting domains into and across the membrane or enhancing the protease resistance of these domains. We now show that some SecA bound at SecYEG is accessible from the periplasm to a membrane-impermeant probe in cells with a permeabilized outer membrane but an intact plasma membrane.
Topological Analysis of
Chlamydia trachomatis
L2 Outer Membrane Protein 2
Authors: Mygind Per , Christiansen Gunna , Birkelund Svend 
Published: December 2019

ABSTRACT

Using monospecific polyclonal antisera to different parts of
Chlamydia trachomatis
L2 outer membrane protein 2 (Omp2), we show that the protein is localized at the inner surface of the outer membrane. Omp2 becomes immunoaccessible when
Chlamydia
elementary bodies are treated with dithiothreitol, and protease digestions indicate that Omp2 has a possible two-domain structure.
Nucleotide Excision Repair in the Third Kingdom
Authors: Ögrünç Müge , Becker Donald F. , Ragsdale Stephen W. , Sancar Aziz 
Published: December 2019

ABSTRACT

Nucleotide excision repair, a general repair mechanism for removing DNA damage, is initiated by dual incisions bracketing the lesion. In procaryotes, the dual incisions result in excision of the damage in 12- to 13-nucleotide-long oligomers, and in eucaryotes they result in excision of the damage in the form of 24- to 32-nucleotide-long oligomers. We wished to find out if
Archaea
perform excision repair. Using cell extracts from
Methanobacterium thermoautotrophicum
, we found that this organism removes UV-induced (6-4) photoproducts in the form of 10- to 11-mers by incising the sixth to seventh phosphodiester bond 5′ to the damage and the fourth phosphodiester bond 3′ to the damage.
Escherichia coli
DNA Topoisomerase I and Suppression of Killing by Tn
5
Transposase Overproduction: Topoisomerase I Modulates Tn
5
Transposition
Authors: Yigit Hesna , Reznikoff William S. 
Published: December 2019

ABSTRACT

Tn
5
transposase (Tnp) overproduction is lethal to
Escherichia coli
. The overproduction causes cell filamentation and abnormal chromosome segregation. Here we present three lines of evidence strongly suggesting that Tnp overproduction killing is due to titration of topoisomerase I. First, a suppressor mutation of transposase overproduction killing,
stkD10
, is localized in
topA
(the gene for topoisomerase I). The
stkD10
mutant has the following characteristics: first, it has an increased abundance of topoisomerase I protein, the topoisomerase I is defective for the DNA relaxation activity, and DNA gyrase activity is reduced; second, the suppressor phenotype of a second mutation localized in
rpoH
,
stkA14
(H. Yigit and W. S. Reznikoff, J. Bacteriol. 179:1704–1713, 1997), can be explained by an increase in
topA
expression; and third, overexpression of wild-type
topA
partially suppresses the killing. Finally, topoisomerase I was found to enhance Tn
5
transposition up to 30-fold in vivo.
A Combination of Three Mutations,
dcd
,
pyrH
, and
cdd
, Establishes Thymidine (Deoxyuridine) Auxotrophy in
thyA
+
Strains of
Salmonella typhimurium
Authors: Krogan Nevan J. , Zaharik Michelle L. , Neuhard Jan , Kelln Rod A. 
Published: December 2019

ABSTRACT

The
dum
gene of
Salmonella typhimurium
was originally identified as a gene involved in dUMP synthesis (C. F. Beck et al., J. Bacteriol. 129:305–316, 1977). In the genetic background used in their selection, the joint acquisition of a
dcd
(dCTP deaminase) and a
dum
mutation established a condition of thymidine (deoxyuridine) auxotrophy. In this study, we show that
dum
is identical to
pyrH
, the gene encoding UMP kinase. The level of UMP kinase activity in the
dum
mutant was found to be only 30% of that observed for the
dum
+
strain. Thymidine prototrophy was restored to the original
dum dcd
mutant (KP1361) either by transduction using a
pyrH
+
donor or by complementation with either of two
pyrH
+
-carrying plasmids. Thymidine auxotrophy could be reconstructed in the
dum
+
derivative (KP1389) by the introduction of a mutant
pyrH
allele. To define the minimal mutational complement necessary to produce thymidine auxotrophy in
thyA
+
strains, a
dcd
::Km null mutation was constructed. In the wild-type background,
dcd
::Km alone or in combination with a
pyrH
(
dum
) mutation did not result in a thymidine requirement. A third mutation,
cdd
(cytidine-deoxycytidine deaminase), was required together with the
dcd
and
pyrH
mutations to impart thymidine auxotrophy.
Autolysis ofLactococcus lactisIs Influenced by Proteolysis
Authors: Buist Girbe , Venema Gerard , Kok Jan 
Published: December 2019

ABSTRACTThe autolysin AcmA ofLactococcus lactiswas shown to be degraded by the extracellular lactococcal proteinase PrtP. Autolysis, as evidenced by reduction in optical density of a stationary-phase culture and concomitant release of intracellular proteins, was greatly reduced whenL. lactisMG1363 cells expressed the cell wall-anchored lactococcal proteinase PrtP of the PI-type caseinolytic specificity (PI). On the other hand, lactococcal strains that did not produce the proteinase showed a high level of autolysis, which was also observed when the cells produced the secreted form of PI or a cell wall-anchored proteinase with PIII-type specificity. Autolysis was also increased when MG1363 expressed the cell wall-anchored hybrid PI/PIII-type proteinase PIac. Zymographic analysis of AcmA activity during stationary phase showed that AcmA was quickly degraded by PI and much more slowly by PrtP proteinases with PIII-type and intermediate specificities. Autolysis ofL. lactisby AcmA was influenced by the specificity, amount, and location of the lactococcal proteinase. No autolysis was observed when the various proteinases were expressed in anL. lactis acmAdeletion mutant, indicating that PrtP itself did not cause lysis of cells. The chain length of a strain was significantly shortened when the strain expressed a cell wall-anchored active proteinase.
Effect of
minCD
on FtsZ Ring Position and Polar Septation in
Bacillus subtilis
Authors: Levin Petra Anne , Shim John Jaeyoung , Grossman Alan D. 
Published: December 2019

ABSTRACT

We examined the pattern of FtsZ localization in a
Bacillus subtilis minCD
mutant. When grown in minimal medium, the majority (∼89%) of the
minCD
mutant cells with an FtsZ ring had a single, medially positioned FtsZ ring. These results indicate that genes in addition to
minCD
function to restrict the number and position of FtsZ rings. When grown in rich medium, greater than 50% of the
minCD
mutant cells had multiple FtsZ rings, indicating significant differences in regulation of FtsZ ring formation based on growth medium.
Sequence Divergence of Seryl-tRNA Synthetases in Archaea
Authors: Kim Hyun-soo , Vothknecht Ute C. , Hedderich Reiner , Celic Ivana , Söll Dieter 
Published: December 2019

ABSTRACT

The genomic sequences of
Methanococcus jannaschii
and
Methanobacterium thermoautotrophicum
contain a structurally uncommon seryl-tRNA synthetase (SerRS) sequence and lack an open reading frame (ORF) for the canonical cysteinyl-tRNA synthetase (CysRS). Therefore, it is not clear if Cys-tRNA
Cys
is formed by direct aminoacylation or by a transformation of serine misacylated to tRNA
Cys
. To address this question, we prepared SerRS from two methanogenic archaea and measured the enzymatic properties of these proteins. SerRS was purified from
M. thermoautotrophicum
; its N-terminal peptide sequence matched the sequence deduced from the relevant ORF in the genomic data of
M. thermoautotrophicum
and
M. jannaschii
. In addition, SerRS was expressed from a cloned
Methanococcus maripaludis serS
gene. The two enzymes charged serine to their homologous tRNAs and also accepted
Escherichia coli
tRNA as substrate for aminoacylation. Gel shift experiments showed that
M. thermoautotrophicum
SerRS did not mischarge tRNA
Cys
with serine. This indicates that Cys-tRNA
Cys
is formed by direct acylation in these organisms.
Inhibition of Development of
Myxococcus xanthus
by Eukaryotic Protein Kinase Inhibitors
Authors: Jain Ritu , Inouye Sumiko 
Published: December 2019

ABSTRACT

Myxococcus xanthus
is a social bacterium that lives in the soil and undergoes spectacular development to form multicellular fruiting bodies. It contains a large family of eukaryote-like serine/threonine protein kinases. We found that a number of inhibitors for eukaryotic protein serine, threonine, and tyrosine kinases could inhibit the development and sporulation of
M. xanthus
to various degrees. These results suggest that serine/threonine and tyrosine phosphorylation may be involved in development of
M. xanthus
. None of the inhibitors tested had any effect on vegetative growth of
M. xanthus
. Most of them seemed to act during the early stages of development. However, the expression of a very early development-specific gene, Ω4521, was not significantly affected by the inhibitors. The patterns of protein phosphorylation during development were also not significantly altered by the inhibitors, suggesting that the targets of the inhibitors are minor or unstable phosphoproteins but play key roles in fruiting-body formation in
M. xanthus.
The
yvyD
Gene of
Bacillus subtilis
Is under Dual Control of ς
B
and ς
H
Authors: Drzewiecki Kathrin , Eymann Christine , Mittenhuber Gerhard , Hecker Michael 
Published: December 2019

ABSTRACT

During a search by computer-aided inspection of two-dimensional (2D) protein gels for ς
B
-dependent general stress proteins exhibiting atypical induction profiles, a protein initially called Hst23 was identified as a product of the
yvyD
gene of
Bacillus subtilis
. In addition to the typical ς
B
-dependent, stress- and starvation-inducible pattern,
yvyD
is also induced in response to amino acid depletion. By primer extension of RNA isolated from the wild-type strain and appropriate mutants carrying mutations in the
sigB
and/or
spo0H
gene, two promoters were mapped upstream of the
yvyD
gene. The ς
B
-dependent promoter drives expression of
yvyD
under stress conditions and after glucose starvation, whereas a ς
H
-dependent promoter is responsible for
yvyD
transcription following amino acid limitation. Analysis of Northern blots revealed that
yvyD
is transcribed monocistronically and confirmed the conclusions drawn from the primer extension experiments. The analysis of the protein synthesis pattern in amino acid-starved wild-type and
relA
mutant cells showed that the YvyD protein is not synthesized in the
relA
mutant background. It was concluded that the stringent response plays a role in the activation of ς
H
. The
yvyD
gene product is homologous to a protein which might modify the activity of ς
54
in gram-negative bacteria. The expression of a ς
L
-dependent (ς
L
is the equivalent of ς
54
in
B. subtilis
)
levD-lacZ
fusion is upregulated twofold in a
yvyD
mutant. This indicates that the
yvyD
gene product, being a member of both the ς
B
and ς
H
regulons, might negatively regulate the activity of the ς
L
regulon. We conclude that (i) systematic, computer-aided analysis of 2D protein gels is appropriate for the identification of genes regulated by multiple transcription factors and that (ii) YvyD might form a junction between the ς
B
and ς
H
regulons on one side and the ς
L
regulon on the other.
Comparison In Vitro of a High- and a Low-Abundance Chemoreceptor of
Escherichia coli
: Similar Kinase Activation but Different Methyl-Accepting Activities
Authors: Barnakov Alexander N. , Barnakova Ludmila A. , Hazelbauer Gerald L. 
Published: December 2019

ABSTRACT

In
Escherichia coli
, high-abundance chemoreceptors are present in cellular amounts approximately 10-fold greater than low-abundance chemoreceptors. Cells containing only low-abundance receptors exhibit abnormally low tumble frequencies and do not migrate effectively in spatial gradients. These defects reflect an inherent activity difference between the two receptor classes. We used in vitro assays to investigate this difference. The low-abundance receptor Trg mediated an ∼100-fold activation of the kinase CheA, only twofold less than activation by the high-abundance receptor Tar. In contrast, Trg was less than 1/20 as active as Tar for in vitro methylation. As observed for high-abundance receptors, kinase activation by Trg varied with the extend of modification at methyl-accepting sites; low methylation corresponded to low kinase activation. Thus, in Trg-only cells, low receptor methylation would result in low kinase activation, correspondingly low content of phospho-CheY, and a decreased dynamic range over which attractant binding could modulate kinase activity. These features could account for the low tumble frequency and inefficient taxis exhibited by Trg-only cells. Thus, the crucial functional difference between the receptor classes is likely to be methyl-accepting activity. We investigated the structural basis for this functional difference by introducing onto the carboxy terminus of Trg a CheR-binding pentapeptide, usually found only at the carboxy termini of high-abundance receptors. This addition enhanced the in vitro methyl-accepting activity of Trg 10-fold.
Identification of
Campylobacter jejuni
Promoter Sequences
Authors: Wösten Marc M. S. M. , Boeve Miranda , Koot Mirjam G. A. , van Nuenen Ad C. , van der Zeijst Bernard A. M. 
Published: December 2019

ABSTRACT

A promoterless
lacZ
shuttle vector, which allowed screening of promoters by β-galactosidase activity in
Campylobacter jejuni
and
Escherichia coli
, was developed. Chromosomal DNA fragments from
C. jejuni
were cloned into this vector; 125 of 1,824 clones displayed promoter activity in
C. jejuni
. Eleven clones with strong promoter activity in
C. jejuni
were further characterized. Their nucleotide sequences were determined, and the transcriptional start sites of the putative promoters in
C. jejuni
were determined by primer extension. Only 6 of these 11 promoters were functional in
E. coli
. The 11 newly characterized and 10 previously characterized
C. jejuni
promoters were used to establish a consensus sequence for
C. jejuni
promoters. The 21 promoters were found to be very similar. They contain three conserved regions, located approximately 10, 16, and 35 bp upstream of the transcriptional start point. The −10 region resembles that of a typical ς
70
E. coli
promoter, but the −35 region is completely different. In addition a −16 region typical for gram-positive bacteria was identified.
The
lytE
Gene of
Bacillus subtilis
168 Encodes a Cell Wall Hydrolase
Authors: Margot Philippe , Wahlen Michael , Gholamhuseinian Ahmad , Piggot Patrick , Karamata Dimitri 
Published: December 2019

ABSTRACT

Bacillus subtilis
cell wall-bound protein CWBP33 is encoded by
lytE
, a gene expressed during the exponential growth phase. Sequence analysis of LytE, a 33-kDa protein, reveals two domains. The N-terminal domain contains a threefold-repeated motif common to several peptidoglycan binding proteins, while the C-terminal domain, probably carrying the catalytic activity, has homology with certain exoproteins. Zymographs unambiguously reveal that the absence of CWBP33, due to inactivation of
lytE
, is accompanied by the loss of a lytic activity. In
lytE
mutants, the cell autolysis rate is significantly decreased, although autolysis of corresponding, purified cell walls does not seem to be affected.
Roles of FtsA and FtsZ in Activation of Division Sites
Authors: Begg Ken , Nikolaichik Yevgeny , Crossland Nicola , Donachie William D. 
Published: December 2019

ABSTRACT
Increasing FtsZ induces the formation of minicells at cell poles but does not increase the frequency or timing of central divisions. A coordinate increase in both FtsZ and FtsA, however, increases the frequency of both polar and central divisions.
Ordered Cloned DNA Map of the Genome of
Vibrio cholerae
569B and Localization of Genetic Markers
Authors: Chatterjee Soma , Mondal Asim K. , Begum Nasim A. , Roychoudhury Susanta , Das Jyotirmoy 
Published: December 2019

ABSTRACT

By using a low-resolution macrorestriction map as the foundation (R. Majumder et al., J. Bacteriol. 176:1105–1112, 1996), an ordered cloned DNA map of the 3.2-Mb chromosome of the hypertoxinogenic strain 569B of
Vibrio cholerae
has been constructed. A cosmid library the size of about 4,000 clones containing more than 120 Mb of
V. cholerae
genomic DNA (40-genome equivalent) was generated. By combining landmark analysis and chromosome walking, the cosmid clones were assembled into 13 contigs covering about 90% of the
V. cholerae
genome. A total of 92 cosmid clones were assigned to the genome and to regions defined by
Not
I,
Sfi
I, and
Ceu
I macrorestriction maps. Twenty-seven cloned genes, 9
rrn
operons, and 10 copies of a repetitive DNA sequence (IS
1004
) have been positioned on the ordered cloned DNA map.
New Flagellin-Specifying Genes in Some
Escherichia coli
Strains
Authors: Ratiner Yuli A. 
Published: December 2019

ABSTRACT

Data for further development of the flagellar antigen genetics of the species
Escherichia coli
are reported. Two new flagellin genes named
fllA
and
flmA
were found in
E. coli
781-55, E2987-73, and E223-69, the test strains for
E. coli
flagellar antigens H44, H55, and H54, respectively (collection of the International
Escherichia
and
Klebsiella
Centre of the World Health Organization, Copenhagen, Denmark). Two alleles of
fllA
were identified that encode flagellar antigens H44 (
fllA
44
) and H55 (
fllA
55
), and the only
flmA
allele found (
flmA
54
) encodes antigen H54. The sites of their integration in the
E. coli
K-12 chromosome after P1-mediated transduction were approximately determined and found to be separate from each other and from the known regions of flagellar genes of
E. coli
and salmonellae. The region of
flm
54
was found to repress the expression of some alleles of the flagellin gene
fliC
. In addition, cryptic genes encoding antigens H4 and H38 were found in phenotypically monophasic test strains 781-55 and E2987-73, respectively.
Evolutionary Relationship between Chlorocatechol Catabolic Enzymes from
Rhodococcus opacus
1CP and Their Counterparts in Proteobacteria: Sequence Divergence and Functional Convergence
Authors: Eulberg Dirk , Kourbatova Elena M. , Golovleva Ludmila A. , Schlömann Michael 
Published: December 2019

ABSTRACT

Biochemical investigations of the muconate and chloromuconate cycloisomerases from the chlorophenol-utilizing strain
Rhodococcus opacus
(
erythropolis
) 1CP had previously indicated that the chlorocatechol catabolic pathway of this strain may have developed independently from the corresponding pathways of proteobacteria. To test this hypothesis, we cloned the chlorocatechol catabolic gene cluster of strain 1CP by using PCR with primers derived from sequences of N termini and peptides of purified chlorocatechol 1,2-dioxygenase and chloromuconate cycloisomerase. Sequencing of the clones revealed that they comprise different parts of the same gene cluster in which five open reading frames have been identified. The
clcB
gene for chloromuconate cycloisomerase is transcribed divergently from a gene which codes for a LysR-type regulatory protein, the presumed ClcR. Downstream of
clcR
but separated from it by 222 bp, we detected the
clcA
and
clcD
genes, which could unambiguously be assigned to chlorocatechol 1,2-dioxygenase and dienelactone hydrolase. A gene coding for a maleylacetate reductase could not be detected. Instead, the product encoded by the fifth open reading frame turned out to be homologous to transposition-related proteins of IS
1031
and Tn
4811
. Sequence comparisons of ClcA and ClcB to other 1,2-dioxygenases and cycloisomerases, respectively, clearly showed that the chlorocatechol catabolic enzymes of
R. opacus
1CP represent different branches in the dendrograms than their proteobacterial counterparts. Thus, while the sequences diverged, the functional adaptation to efficient chlorocatechol metabolization occurred independently in proteobacteria and gram-positive bacteria, that is, by functionally convergent evolution.