bluuebunny/crossref_metadata_2025_split huggingface dataset:
New evidence supports the prophage origin of RcGTA
Authors: Xu Yongle , Liu Binbin , Jiao Nianzhi , Liu Jihua , Chen Feng 
Published: August 2024

ABSTRACT

Gene transfer agents (GTAs) are phage-like entities that package and transfer random host genome fragments between prokaryotes. RcGTA, produced by
Rhodobacter capsulatus
, is hypothesized to originate from a prophage ancestor. Most of the evidence supporting this hypothesis came from the finding of RcGTA-like genes in phages. More than 75% of the RcGTA genes have a phage homolog. However, only a few RcGTA homologs have been identified in a (pro)phage genome, leaving the hypothesis that GTAs evolved from prophages through gene loss with only weak evidence. We herein report the discovery of an inducible prophage (vB_MseS-P1) from a
Mesorhizobium sediminum
strain that contains the largest number (12) of RcGTA homologs found in a phage genome to date. We also identified three putative prophages and two prophage remnants harboring 12–14 RcGTA homologs in a
Methylobacterium nodulans
strain. The protein remote homology detection also revealed more RcGTA homologs from other phages than we previously thought. Moreover, the head–tail gene architecture of these newly discovered prophage-related elements closely resembles that of RcGTA. Furthermore, vB_MseS-P1 virions have structural proteins similar to RcGTA particles. Close phylogenetic relationships between certain prophage genes and RcGTA-like genes in Alphaproteobacteria further support the shared ancestry between RcGTA and prophages. Our findings provide new relatively direct evidence of the origin of RcGTA from a prophage progenitor.

IMPORTANCE
GTAs are important genetic elements in certain groups of bacteria and contribute to the genetic diversification, evolution, and ecological adaptation of bacteria. RcGTA, a common type of GTA, is known to package and transfer random fragments of the bacterial genome to recipient cells. However, the origin of RcGTA is still elusive. It has been hypothesized that RcGTA evolved from a prophage ancestor through gene loss. However, the few RcGTA homologs identified in a (pro)phage genome leave the hypothesis lacking direct evidence. This study uncovers the presence of a large number of RcGTA homologs in an inducible prophage and several putative prophages. The similar head–tail gene architecture and structural protein compositions of these newly discovered prophage-related elements and RcGTA further demonstrate an unprecedentedly observed close evolutionary relationship between prophages and RcGTA. Together, our findings provide more direct evidence supporting the origin of RcGTA from prophage.
Complete genome sequences of
Clostridium perfringens
CP201 isolated from an asymptomatic rhesus monkey (
Macaca mulatta
)
Authors: Kim Sung Guk , Wang Sharon X. , Park Miseon , Min Seonggi , Foley Steven L. 
Published: August 2024

ABSTRACT

Clostridium perfringens
is a leading cause of human gastroenteritis. The genome sequence of
C. perfringens
CP201 from an asymptomatic rhesus monkey,
Macaca mulatta
, consists of one chromosome (3,241,413 bp; 30.22% G + C) and one plasmid (92,983 bp; 28.43% G + C), encoding 2,935 genes, 94 tRNAs, 30 rRNAs, and 1 CRISPR array.
Identification and characterization of archaeal-type FAD synthase as a novel tractable drug target from the parasitic protozoa
Entamoeba histolytica
Authors: Wulansari Dewi , Jeelani Ghulam , Yazaki Euki , Nozaki Tomoyoshi 
Published: August 2024

ABSTRACT

Flavin adenine dinucleotide (FAD) is an essential cofactor for numerous flavoenzymes present in all living organisms. The biosynthesis of FAD from riboflavin involves two sequential reactions catalyzed by riboflavin kinase and flavin adenine dinucleotide synthase (FADS).
Entamoeba histolytica
, the protozoan parasite responsible for amebiasis, apparently lacks a gene encoding FADS that share similarity with bacterial and eukaryotic canonical FADS, yet it can synthesize FAD. In this study, we have identified the gene responsible for FADS and thoroughly characterized physiological and biochemical properties of FADS from
E. histolytica
. Phylogenetic analysis revealed that the gene was likely laterally transferred from archaea. The kinetic properties of recombinant EhFADS were consistent with the notion that EhFADS is of archaeal origin, exhibiting
K
M
and
k
cat
values similar to those of the arachaeal enzyme while significantly differing from the human counterpart. Repression of gene expression of
EhFADS
by epigenetic gene silencing caused substantial reduction in FAD levels and parasite growth, underscoring the importance of EhFADS for the parasite. Furthermore, we demonstrated that
EhFADS
gene silencing reduced thioredoxin reductase activity, which requires FAD as a cofactor and makes the ameba more susceptible to metronidazole. In summary, this study unveils unique evolutionary and biochemical features of EhFADS and underscores its significance as a promising drug target in combating human amebiasis.

IMPORTANCE

FAD is important for all forms of life, yet its role and metabolism are still poorly studied in
E. histolytica
, the protozoan parasite causing human amebiasis. Our study uncovers the evolutionary unique key enzyme, archaeal-type FADS for FAD biosynthesis from
E. histolytica
for the first time. Additionally, we showed the essentiality of this enzyme for parasite survival, highlighting its potential as target for drug development against
E. histolytica
infections.
Transcription factors containing both C
2
H
2
and homeobox domains play different roles in
Verticillium dahliae
Authors: Tang Chen , Wang Haifeng , Jin Xianjiang , Li Wenwen , Wang Yonglin 
Published: August 2024

ABSTRACT

Verticillium dahliae
causes Verticillium wilt in more than 200 plant species worldwide. As a soilborne fungus, it forms melanized microsclerotia and colonizes the xylem of host plants. Our previous study revealed a subfamily of C
2
H
2
-homeobox transcription factors in
V. dahliae
, but their biological roles remain unknown. In this study, we systematically characterized the functions of seven C
2
H
2
-homeobox transcription factors in
V. dahliae
. Deletion of
VdChtf3
and
VdChtf6
significantly decreased the production of melanized microsclerotia, and knockout of
VdChtf1
and
VdChtf4
enhanced virulence. Loss of
VdChtf2
and
VdChtf6
increased conidium production, whereas loss of
VdChtf5
and
VdChtf7
did not affect growth, conidiation, microsclerotial formation, or virulence. Further research showed that VdChtf3 activated the expression of genes encoding pectic enzymes to participate in microsclerotial formation. In addition, VdChtf4 reduced the expression of
VdSOD1
to disturb the scavenging of superoxide radicals but induced the expression of genes related to cell wall synthesis to maintain cell wall integrity. These findings highlight the diverse roles of different members of the C
2
H
2
-homeobox gene family in
V. dahliae
.

IMPORTANCE

Verticillium dahliae
is a soilborne fungus that causes plant wilt and can infect a variety of economic crops and woody trees. The molecular basis of microsclerotial formation and infection by this fungus remains to be further studied. In this study, we analyzed the functions of seven C2H2-homobox transcription factors. Notably, VdChtf3 and VdChtf4 exhibited the most severe defects, affecting phenotypes associated with critical developmental stages in the
V. dahliae
disease cycle. Our results indicate that VdChtf3 is a potential specific regulator of microsclerotial formation, modulating the expression of pectinase-encoding genes. This finding could contribute to a better understanding of microsclerotial development in
V. dahliae
. Moreover, VdChtf4 was associated with cell wall integrity, reactive oxygen species (ROS) stress resistance, and increased virulence. These discoveries shed light on the biological significance of C2H2-homeobox transcription factors in
V. dahliae
's adaptation to the environment and infection of host plants.
Investigating group A
Streptococcus
antibiotic tolerance in necrotizing fasciitis
Authors: Keller Nadia , Boumasmoud Mathilde , Andreoni Federica , Tarnutzer Andrea , von Matt Manuela , Scheier Thomas C. , Epprecht Jana , Weller David , Gómez-Mejia Alejandro , Huemer Markus , von Reibnitz Donata , Fontein Duveken B. Y. , Marques-Maggio Ewerton , Schuepbach Reto A. , Mairpady-Shambat Srikanth , Brugger Silvio D. , Zinkernagel Annelies S. 
Published: August 2024

ABSTRACT

Group A
Streptococcus
(GAS) necrotizing fasciitis (NF) is a difficult-to-treat bacterial infection associated with high morbidity and mortality despite extensive surgery and targeted antibiotic treatment. Difficult-to-treat infections are often characterized by the presence of bacteria surviving prolonged antibiotic exposure without displaying genetic resistance, referred to as persisters. In the present study, we investigated the presence of GAS persisters in tissue freshly debrided from patients as well as in an
in vivo
mouse model of NF and examined the phenomenon of antibiotic tolerance. Time-lapse imaging of GAS plated directly upon isolation from NF debrided tissue and an antibiotic challenge-based persisters assay were used to assess the presence of persisters. We show for the first time that GAS recovered directly from freshly debrided NF tissue is characterized by heterogeneous and overall delayed colony appearance time, suggesting the presence of persisters. Acidic pH or nutrient stress exposure, mimicking the NF-like environment
in vitro
, led to a similar phenotypic heterogeneity and resulted in enhanced survival upon antibiotic challenge, confirming the presence of GAS persisters. GAS persisters might contribute to NF treatment failure, despite extensive surgery and adequate antibiotic treatment.

IMPORTANCE

Difficult-to-treat and recurrent infections are a global problem burdening society and the health care system alike. Unraveling the mechanisms by which bacteria can survive antibiotic treatment without developing genetic resistance is of utmost importance to lay the foundation for new, effective therapeutic approaches. For the first time, we describe the phenomenon of antibiotic tolerance in group A
Streptococcus
(GAS) isolated from necrotizing fasciitis (NF) patients. Dormant, non-replicating cells (persisters) are tolerant to antibiotics and their occurrence
in vivo
is reported in an increasing number of bacterial species. Tailored treatment options, including the use of persisters-targeting drugs, need to be developed to specifically target dormant bacteria causing difficult-to-treat and recurrent infections.
Minimal transcriptional regulation of horizontally transferred photosynthesis genes in phototrophic bacterium
Gemmatimonas phototrophica
Authors: Kopejtka Karel , Tomasch Jürgen , Shivaramu Sahana , Saini Mohit Kumar , Kaftan David , Koblížek Michal 
Published: August 2024

ABSTRACT

The first phototrophic member of the bacterial phylum
Gemmatimonadota
,
Gemmatimonas phototrophica
AP64
T
, received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host.
G. phototrophica
grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of
G. phototrophica
was optimal at 80 µmol photon m
−2
s
−1
, while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark–light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m
−2
s
−1
) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that
G. phototrophica
possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead,
G. phototrophica
has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms.

IMPORTANCE

Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient’s cellular machinery.
Gemmatimonas phototrophica
, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that
G. phototrophica
lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.
Characterization of novel double-reporter strains of
Mycobacterium abscessus
for drug discovery: a study in mScarlet
Authors: Bento Clara M. , van Calster Kevin , Piller Tatiana , Oliveira Gabriel S. , de Vooght Linda , Cappoen Davie , Cos Paul , Gomes M. Salomé , Silva Tânia 
Published: August 2024

ABSTRACT

Mycobacterium abscessus
(Mab) is an emerging pathogen that poses a severe health threat, especially in people with cystic fibrosis and other chronic lung diseases. Available drugs are largely ineffective due to an exquisite intrinsic resistance, making Mab infections only comparable to multidrug-resistant tuberculosis. Current treatment is based on lengthy multidrug therapy, complicated by poor outcomes and high rates of treatment failure, recurrence, and mortality. Thus, finding new and more efficient drugs to combat this pathogen is urgent. However, drug discovery efforts targeting Mab have been limited, and traditional drug screening methods are labor-intensive, low-throughput, and do not reflect clinical effectiveness. Therefore, this work aimed to develop a new, efficient, and reliable tool for drug screening against Mab that can be used
in vitro
for identifying hits in a high-throughput manner and
in vivo
to select drug candidates for future clinical trials. We engineered two stable double-reporter strains of Mab capable of emitting strong fluorescent and luminescent signals. This is due to the expression of mScarlet protein and luciferase enzyme or the entire lux operon. Importantly, these strains maintain the same ground characteristics as the non-transformed Mab strain. We show that these new strains can be applied to various setups, from MIC determination in broth cultures and macrophage infection assays to
in vivo
infection (using the
Galleria mellonella
model). Using these strains enhances the potential for high-throughput screening of thousands of compounds in a fast and reliable way.

IMPORTANCE

Mycobacterium abscessus
(Mab) is currently considered an “incurable nightmare.” Its intrinsic resistance, high toxicity, long duration, and low cure rates of available therapies often lead to the clinical decision not to treat. Moreover, one of the significant drawbacks of anti-Mab drug development is the lack of correlation between
in vitro
susceptibility and clinical efficacy. Most drug screening assays are performed on Mab growing in liquid cultures. But being an intracellular pathogen, inducing granulomas and biofilm formation, the broth culture is far from ideal as
in vitro
drug-testing setup. This study presents new double-reporter Mab strains that allow direct real-time bacterial detection and quantification in a non-invasive way. These strains can be applied to an extensive range of experimental settings, far surpassing the utility of single-reporter bacteria. They can be used in all steps of the pre-clinical anti-Mab drug development pipeline, constituting a highly valuable tool to increase its success.
Assessment of Left Atrial Fibrosis by Cardiac Magnetic Resonance Imaging in Ischemic Stroke Patients Without Atrial Fibrillation: A Systematic Review and Meta‐Analysis
Authors: Koh Jin Hean , Lim Lincoln Kai En , Tan Ying Kiat , Goh Claire , Teo Yao Hao , Ho Jamie Sin Ying , Dalakoti Mayank , Chan Mark Yan Yee , Sia Ching‐Hui , Yeo Leonard Leong Litt , Tan Benjamin Yong Qiang 
Published: August 2024

Background
Left atrial (LA) fibrosis is a marker of atrial cardiomyopathy and has been reported to be associated with both atrial fibrillation and ischemic stroke. Elucidating this relationship is clinically important as LA fibrosis could serve as a surrogate biomarker of LA cardiomyopathy. The objective of this study is to investigate the association of LA fibrosis and embolic stroke of undetermined source (ESUS) using cardiac magnetic resonance imaging.

Methods and Results

Following an International Prospective Register of Systematic Reviews‐registered protocol, 3 blinded reviewers performed a systematic review for studies that quantified the degree of LA fibrosis in patients with ESUS as compared with healthy patients from inception to February 2024. A meta‐analysis was conducted in the mean difference. From 7 studies (705 patients), there was a significantly higher degree of LA fibrosis in patients with ESUS compared with healthy controls (MD, 5.71% [95% CI, 3.55%–7.87%],
P
<0.01). The degree of LA fibrosis was significantly higher in patients with atrial fibrillation than healthy controls (MD, 8.22% [95% CI, 5.62%–10.83%],
P
<0.01). A similar degree of LA fibrosis was observed in patients with ESUS compared with patients with atrial fibrillation (MD, −0.92% [95% CI, −2.29% to 0.44%],
P
=0.35).

Conclusions
A significantly higher degree of LA fibrosis was found in patients with ESUS as compared with healthy controls. This suggests that LA fibrosis may play a significant role in the pathogenesis of ESUS. Further research is warranted to investigate LA fibrosis as a surrogate biomarker of atrial cardiomyopathy and recurrent stroke risk in patients with ESUS.
Left Atrial Appendage Opacification on Cardiac Computed Tomography in Acute Ischemic Stroke: The Clinical Implications of Slow‐Flow
Authors: Nio Shan Sui , Rinkel Leon A. , Cramer Olivia N. , Özata Z. Beyda , Beemsterboer Chiel F. P. , Guglielmi Valeria , Bouma Berto J. , Boekholdt S. Matthijs , Lobé Nick H. J. , Beenen Ludo F. M. , Marquering Henk A. , Majoie Charles B. L. M. , Roos Yvo B. W. E. M. , van Randen Adrienne , Planken R. Nils , Coutinho Jonathan M. 
Published: August 2024

Background
Left atrial appendage (LAA) slow‐flow may increase the risk of ischemic stroke. We studied LAA attenuation on cardiac computed tomography in patients with acute ischemic stroke.

Methods and Results

We used data from a prospective cohort of patients with acute ischemic stroke undergoing cardiac computed tomography during the acute stroke imaging protocol. We compared characteristics, functional outcome (modified Rankin scale: higher scores indicating worse outcome), stroke recurrence and major adverse cardiovascular events after 2‐year follow‐up between patients with LAA thrombus (filling defect<100 Hounsfield Unit (HU)), slow‐flow (filling defect ≥100 HU) and normal filling. Of 421 patients, 31 (7%) had LAA thrombus, 69 (16%) slow‐flow, and 321 (76%) normal filling. Patients with thrombus or slow‐flow more often had known atrial fibrillation compared with normal filling (45%, 39%, and 9%,
P
<0.001). Patients with thrombus had higher National Institutes of Health Stroke Scale‐scores compared with slow‐flow and normal filling (18 [interquartile range, 9–22], 6 [interquartile range, 3–17], and 5 [interquartile range, 2–11],
P
<0.001). Compared with normal filling, there was no difference with slow‐flow in functional outcome (median modified Rankin scale, 3 versus 2; acOR 0.8 [95% CI, 0.5–1.4]), stroke recurrence (adjusted hazard ratio, 0.8 [95% CI, 0.3–1.9]) or major adverse cardiovascular events (adjusted hazard ratio, 1.2 [95% CI, 0.7–2.1]), while patients with thrombus had worse functional outcome (median modified Rankin scale, 6, acOR, 3.3 [95% CI, 1.5–7.4]). In cryptogenic stroke patients (n=156) slow‐flow was associated with stroke recurrence (27% versus 6%, aHR, 4.1 [95% CI, 1.1–15.7]).

Conclusions
Patients with slow‐flow had similar characteristics to patients with thrombus, but had less severe strokes. Slow‐flow was not significantly associated with functional outcome or major adverse cardiovascular events, but was associated with recurrent stroke in patients with cryptogenic stroke.
Cardiac Findings Following Cerebrovascular Disease
Authors: Rohner Marco H. , Gebhard Catherine , Luft Andreas , Hänsel Martin , Wegener Susanne 
Published: August 2024

Background
Accumulating evidence suggests that cardiac findings after stroke are an important, yet understudied, manifestation of brain–heart interactions. Our aim was to investigate and compare cardiac findings after different cerebrovascular events (acute ischemic stroke, transient ischemic attack, and hemorrhagic stroke).

Methods and Results

There were 7113 patients screened who were treated between December 2013 and December 2020 at the University Hospital Zurich for ischemic stroke, transient ischemic attack, and hemorrhagic stroke. Seven hundred twenty‐one patients without evidence of previous cardiac disease or presumed cardioembolic origin of their cerebrovascular disease and with at least 1 cardiac checkup were included. Clinical reports from the year following disease onset were screened for new cardiac findings, which were categorized as arrhythmia/electrocardiographic changes, myocardial alterations, valvular abnormalities, and coronary perfusion insufficiency. Differences in proportions of findings among groups were analyzed using the Pearson χ
2
test or Fisher exact test. ECG changes were observed in 81.7% (n=474) of patients with ischemic stroke, 71.4% (n=70) of patients with transient ischemic attack, and 55.8% (n=24) of patients with hemorrhagic stroke (
P
<0.001). Myocardial alterations occurred often in all 3 groups (60.9% ischemic stroke [n=353], 59.2% transient ischemic attack [n=58], 44.2% hemorrhagic stroke [n=19];
P
=0.396).

Conclusions
Cardiac findings are frequent in patients with cerebrovascular disease, even without prior cardiac problems or suspected cardiac cause. Similarities, especially between patients with ischemic stroke and transient ischemic attack, were observed. Our data suggest that all patients with acute cerebrovascular events should receive thorough workup searching for cardiac manifestations.