bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA stability is regulated by both RNA polyadenylation and ATP levels, linking RNA and energy metabolisms in
Escherichia coli
Authors: Roux Charlotte , Ramos-Hue Marvin , Audonnet Marjorie , Duviau Marie-Pierre , Nouaille Sébastien , Carpousis Agamemnon J. , Laguerre Sandrine , Hajnsdorf Eliane , Cocaign-Bousquet Muriel , Girbal Laurence 
Published: November 2024

ABSTRACT

The post-transcriptional process of RNA polyadenylation sits at the crossroads of energy metabolism and RNA metabolism. RNA polyadenylation is catalyzed by poly(A) polymerases, which use ATP as a substrate to add adenine to the 3′ end of RNAs, which can alter their stability. In
Escherichia coli,
RNA polyadenylation mediated by the major poly(A) polymerase was previously shown to facilitate degradation of individual RNAs. In this study, we performed the first genome-wide study of RNA stability in the absence of PAP I. Inactivation of the
pcnB
gene coding for PAP I led to the stabilization of more than a thousand of
E. coli
RNAs in the form of full-length functional molecules or non-functional fragments. The absence of PAP I altered the energy metabolism, with an almost 20% reduction in ATP levels. To better understand how RNA and energy metabolisms are interconnected, we investigated the role of ATP levels in regulating RNA stability. When we lowered intracellular ATP levels below 0.5 mM, many RNAs were stabilized, demonstrating the causal link between ATP levels and RNA stability for the first time in
E. coli
. Above this concentration, changes in ATP levels had no impact on RNA stability. We also demonstrated that some RNAs were stabilized when PAP I was inactivated by low ATP availability. These results clearly demonstrate that PAP I mediates an energy-dependent RNA stabilization, which may contribute to cell energy homeostasis under energy-limited conditions.

IMPORTANCE

Poly(A) polymerases are prime targets for understanding the interactions between RNA polyadenylation, RNA stability, and cellular energy. These enzymes catalyze the process of RNA polyadenylation, which involves ATP hydrolysis and addition of poly(A) tails to the 3′ end of RNAs. 3′ end poly(A) extensions potentially facilitate RNA degradation in bacteria. In this study, we inactivated the
pcnB
gene encoding PAP I, the major poly(A) polymerase in
E. coli
, and investigated the effects on RNA stability and energy levels. Our results show for the first time in
E. coli
a genome-wide RNA stabilization in the absence of PAP I associated with a decrease in ATP levels. We provide the first evidence in
E. coli
of a link between ATP levels and RNA stabilization and demonstrate that this is mediated in some cases by PAP I. PAP I-mediated RNA stabilization at low ATP levels could be a means of energy conservation under energy-limited conditions.
Coatomer complex I is required for the transport of SARS-CoV-2 progeny virions from the endoplasmic reticulum-Golgi intermediate compartment
Authors: Hirabayashi Ai , Muramoto Yukiko , Takenaga Toru , Tsunoda Yugo , Wakazaki Mayumi , Sato Mayuko , Fujita-Fujiharu Yoko , Nomura Norimichi , Yamauchi Koji , Onishi Chiho , Nakano Masahiro , Toyooka Kiminori , Noda Takeshi 
Published: November 2024

ABSTRACT

SARS-CoV-2 undergoes budding within the lumen of the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), and the progeny virions are delivered to the cell surface via vesicular transport. However, the molecular mechanisms remain poorly understood. Using three-dimensional electron microscopic analysis, such as array tomography and electron tomography, we found that virion-transporting vesicles possessed protein coats on their membrane and demonstrated that the protein coat was coatomer complex I (COPI). During the later stages of SARS-CoV-2 infection, we observed a notable alteration in the distribution of COPI and ERGIC throughout the cytoplasm, suggesting their potential involvement in virus replication. Depletion of COPB2, a key component of COPI, led to the confinement of SARS-CoV-2 progeny virions within the ERGIC at the perinuclear region. While the expression levels of viral proteins within cells were comparable, this depletion significantly reduced the efficiency of virion release, leading to the significant reduction of viral replication. Hence, our findings suggest COPI as a critical player in facilitating the transport of SARS-CoV-2 progeny virions from the ERGIC. Thus, COPI could be a promising target for the development of antivirals against SARS-CoV-2.

IMPORTANCE
SARS-CoV-2 virions are synthesized within the ERGIC and are transported to the cell surface via vesicular transport for release. However, the precise mechanisms remain unclear. Through various electron microscopic techniques, we identified the presence of COPI on virion-transporting vesicles. Alterations in the distribution of COPI and ERGIC in SARS-CoV-2 infected cells are evident, suggesting their involvement in virus replication. When COPB2, a component of COPI, is depleted, progeny virions become trapped within the ERGIC, leading to a reduction in the efficiency of virion release. These findings highlight COPI’s crucial role in mediating SARS-CoV-2 vesicular transport from the ERGIC and suggest it as a potential antiviral target.
A whole-genome metagenomic approach to explore the gut microbiome of inflammatory bowel disease patients in Bangladesh
Authors: Siam Md. Hasanul Banna , Mondol Spencer Mark , Shakil Md. Shahriar Kabir , Islam Md. Rafiul , Islam Israt , Saha Otun , Amiruzzaman  , Datta Raj , Ahmed Toufiq , Gomes Donald James , Rahaman Md. Mizanur 
Published: November 2024

ABSTRACT

In this study, we analyzed the gut microbiome of four Bangladeshi
inflammatory bowel disease patients, identifying
Segatella
copri
as the most prevalent, followed by
Phocaeicola
vulgatus
,
Bacteroides xylanisolvens
,
Bacteroides fragilis
,
Bacteroides
thetaiotaomicron
,
Bacteroides ovatus
,
Bacteroides uniformis
,
Phocaeicola
dorei
, and many other species. Firmicutes, Proteobacteria,
Bacteroidetes, and Actinobacteria were the major phyla detected.
Site-selective modifications by lipid A phosphoethanolamine transferases linked to colistin resistance and bacterial fitness
Authors: Schumann Anna , Gaballa Ahmed , Yang Hyojik , Yu Di , Ernst Robert K. , Wiedmann Martin 
Published: November 2024

ABSTRACT

Genes encoding lipid A modifying phosphoethanolamine transferases (PETs) are genetically diverse and can confer resistance to colistin and antimicrobial peptides. To better understand the functional diversity of PETs, we characterized three canonical mobile colistin resistance (
mcr
) alleles (
mcr-1
,
-3
,
-9
), one intrinsic
pet
(
eptA
), and two
mcr
-like genes (
petB
,
petC
) in
Escherichia coli
. Using an isogenic expression system, we show that
mcr-1
and
mcr-3
confer similar phenotypes of decreased colistin susceptibility with low fitness costs.
mcr-9
, which is phylogenetically closely related to
mcr-3
, and
eptA
only provide fitness advantages in the presence of sub-inhibitory concentrations of colistin and significantly reduce fitness in media without colistin. PET-B and PET-C were phenotypically distinct from bonafide PETs; neither impacted colistin susceptibility nor caused considerable fitness cost. Strikingly, we found for the first time that different PETs selectively modify different phosphates of lipid A; MCR-1, MCR-3, and PET-C selectively modify the 4′-phosphate, whereas MCR-9 and EptA modify the 1-phosphate. However, 4′-phosphate modifications facilitated by MCR-1 and -3 are associated with lowered colistin susceptibility and low toxicity. Our results suggest that PETs have a wide phenotypic diversity and that increased colistin resistance is associated with specific lipid A modification patterns that have been largely unexplored thus far.

IMPORTANCE

Rising levels of resistance to increasing numbers of antimicrobials have led to the revival of last resort antibiotic colistin. Unfortunately, resistance to colistin is also spreading in the form of
mcr
genes, making it essential to (i) improve the identification of resistant bacteria to allow clinicians to prescribe effective drug regimens and (ii) develop new combination therapies effective at targeting resistant bacteria. Our results demonstrate that PETs, including MCR variants, are site-selective in
Escherichia coli
and that site-selectivity correlates with the level of susceptibility and fitness costs conferred by certain PETs. Site selectivity associated with a given PET may not only help predict colistin resistance phenotypes but may also provide an avenue to (i) improve drug regimens and (ii) develop new combination therapies to better combat colistin-resistant bacteria.
Direct prion neuroinvasion following inhalation into the nasal cavity
Authors: Kincaid Anthony E. , Clouse Melissa D. , Magrum Shawn M. , Bartz Jason C. 
Published: November 2024

ABSTRACT

Inhalation of prions into the nasal cavity is an efficient route of infection. Following inhalation of infectious prions, animals develop disease with a similar incubation period compared with per os exposure, but with greater efficiency. To identify the reason for this increased efficiency, we identified neural structures that uniquely innervate the nasal cavity and neural structures known to mediate neuroinvasion following oral infection and used immunohistochemistry to determine the temporal and spatial accumulation of prions from hamster tissue sections containing cell bodies and axons at 2-week intervals following prion exposure. Prions were identified in the trigeminal ganglion, the spinal trigeminal tract in the brainstem, the intermediolateral cell column of the thoracic spinal cord, and the dorsal motor nucleus of the vagus/solitary nucleus complex months prior to detection of prions in the olfactory bulb or superior cervical ganglion. These results indicate that the trigeminal nerve, but not the olfactory nerve or sympathetic nerves, are involved in neuroinvasion following inhalation of prions into the nasal cavity. The detection of prions in the intermediolateral cell column of the thoracic spinal cord and dorsal motor nucleus of the vagus nerve 14 weeks following inhalation is consistent with inoculum crossing the alimentary wall and infecting the enteric nervous system via this route of infection. Neuroinvasion via the trigeminal nerve, in combination with entry into the central nervous system via autonomic innervation of the enteric nervous system, may contribute to increased efficiency of nasal cavity exposure to prions compared with per os exposure in hamsters.

IMPORTANCE
Inhalation of prions into the nasal cavity is thought to be a route of infection in naturally acquired prion diseases. Experimental studies indicate that inhalation of prions is up to two orders of magnitude more efficient compared with ingestion. The mechanisms underlying this observation are poorly understood. We found a previously unreported direct route of neuroinvasion from the nasal cavity to the nervous system. Importantly, the peripheral ganglia involved may be a useful tissue to sample for prion diagnostics. Overall, identification of a new route of neuroinvasion following prion infection may provide an anatomical basis to explain the increased efficiency of infection following prion inhalation.
Antimicrobial resistance, virulence gene profiles, and molecular epidemiology of enterococcal isolates from patients with urinary tract infections in Shanghai, China
Authors: Wu Weiyi , Xiao Shuzhen , Han Lizhong , Wu Qiong 
Published: November 2024

ABSTRACT

Urinary tract infections (UTIs) are among the most prevalent infectious diseases, yet there is still limited understanding of the epidemiology of Enterococcal strains isolated from UTI patients in Shanghai. This study aims to elucidate the antimicrobial resistance profiles, virulence gene carriage, and molecular epidemiology of selected Enterococcal strains from UTI patients in Shanghai. A cohort of 80
Enterococcus faecalis
and 40
Enterococcus faecium
clinical isolates were randomly selected from UTI patients from October 2022 to March 2023. No vancomycin-resistant strains were identified based on minimum inhibitory concentration (MIC) testing. However, five strains of linezolid-resistant
E. faecalis
were identified, all of which were confirmed to be
optrA
-positive through whole-genome sequencing (WGS), with ST300 being reported as the first instance of this ST type in China. Polymerase chain reaction (PCR) assays were employed to ascertain the presence of virulence genes and multi-locus sequence type (MLST). In
E. faecalis
, the most common virulence genes were
asal
(75%),
gelE
(65%),
esp
(52.5%), and
cylA
(47.5%). In contrast,
E. faecium
primarily exhibited
esp
(65%) and
hyl
(12.5%). Among the
E. faecalis
strains, 21 distinct MLST types were identified, with ST16 and ST179 prevailing. Conversely,
E. faecium
exhibited only five MLST types, with ST78 being predominant. The prevalence of
E. faecalis
CC16 and
E. faecium
CC17 further complicates the treatment landscape for Enterococcal UTIs.

IMPORTANCE

This study highlighted the critical need to understand Enterococcal strains causing UTIs in Shanghai, given their high prevalence. By assessing antimicrobial resistance profiles, virulence gene presence, and molecular epidemiology, the research offered valuable insights into the local epidemiology of
Enterococcus faecalis
and
Enterococcus. faecium
. Identifying linezolid-resistant strains, all of which carry the
optrA
gene, including the first report of ST300 in China and recognizing dominant MLST types, such as ST16 and ST179 for
E. faecalis
and ST78 for
E. faecium
, are vital for guiding treatment and addressing the challenges these infections present. The data emphasize the need for ongoing surveillance and customized therapeutic approaches to combat emerging resistance and virulence factors in Enterococcal UTIs.
ITS amplicon sequencing revealed that rare taxa of tea rhizosphere fungi are closely related to the environment and provide feedback on tea tree diseases
Authors: Zhao Yuanqi , Ran Weiwei , Xu Wenming , Song Yuehua 
Published: November 2024

ABSTRACT

The rhizospheres of plants and soil microorganisms are intricately interconnected. Tea trees are cultivated extensively on the karst plateau of Guizhou Province, China; however, the understanding of the interactions among fungal communities, community taxa, and diseases impacting tea tree in the soil rhizosphere is limited. Our aim is to offer insights for the advancement of modern agriculture in ecologically fragile karst tea gardens, as well as microbiomics concepts for green and sustainable environmental development. This study utilized the internal transcribed spacer high-throughput sequencing technology to explore the symbiotic relationship between rhizosphere fungi and plant disease feedback in multiple tea estates across the Guizhou Plateau. The ecological preferences and environmental thresholds of fungi were investigated via environmental variables. Furthermore, a correlation was established between different taxa and individual soil functions. Research has indicated that tea leaf blight disrupts symbiotic connections among fungal groups. For various taxa, we found that numerous taxa consistently maintained core positions within the community, whereas rare taxa were able to stabilize due to a high proportion of positive effects. Additionally, abundant taxa presented a wider range of environmental feedback, whereas the rare taxon diversity presented a stronger positive association with the soil Z score. This study contributes to our understanding of the importance of rare taxa in plant rhizosphere soil processes. Emphasis should be placed on the role of rare taxa in pest and disease control within green agriculture while also strengthening systematic development and biogeographical research related to rare taxa in this region.

IMPORTANCE
In this study, based on internal transcribed spacer high-throughput sequencing, fungal communities in the rhizosphere soil of tea trees and their interactions with the environment in karst areas were reported, and the symbiotic relationships of different fungal taxa and their feedback to the environment were described in detail by using the knowledge of microbial ecology. On this basis, it was found that tea tree diseases affect the symbiotic relationships of fungal taxa. At the same time, we found that rare taxa have stronger cooperative relationships in response to environmental changes and explored their participation in soil processes based on fungal trait sets. This study will provide basic data for the development of modern agriculture in tea gardens and theoretical basis for the sustainable prevention and control of tea tree diseases.
Multiomics comparative analysis of feces AMRGs of Duroc pigs and Tibetan and the effect of fecal microbiota transplantation on AMRGs upon antibiotic exposure
Authors: Wang Tao , Luo Yuheng , Kong Xiangfeng , Fang Ling , Zhu Liping , Yu Bing , Zheng Ping , Huang Zhiqing , Mao Xiangbing , Jie Yu , Luo Junqiu , Yan Hui , He Jun 
Published: November 2024

ABSTRACT

Fecal matter is recognized as both a reservoir and a transmission source for various antimicrobial resistance genes (AMRGs). However, the transcriptional activity of AMRGs in swine feces is not well understood. In addition, the effect of fecal microbiota transplantation (FMT) on the excretion of AMRGs has rarely been reported. Our study explored the diversity, abundance, transcriptional activity, and bacterial hosts of AMRGs in Tibetan and Duroc pig feces using metagenomic and metatranscriptomic sequencing technologies. We discovered a significantly higher genomic abundance of AMRGs in the feces of Duroc pigs compared to Tibetan pigs (
P <
0.001), although the transcript levels did not show a significant difference. The results showed that the core composition of AMRGs in pig feces varied considerably, with the most transcriptionally active AMRGs being
oqxB
,
tetQ
,
Bla1
,
dfrA1
, and
amrB
. Furthermore, the
Firmicutes
phylum is the main host of AMRGs. By transplanting fecal flora from Tibetan and Duroc pigs into the intestines of Duroc Landrace Yorkshire (DLY) piglets after acute antibiotic exposure, we found that only Tibetan pig fecal flora significantly reduced AMRGs in the feces of DLY piglets (
P <
0.05). The effectiveness of Tibetan pig fecal microorganisms in removing AMRGs from DLY pig feces was mainly influenced by microbial communities, especially the
Bacteroidota
phylum. These findings offer valuable insights for the prevention and control of AMRG pollution.

IMPORTANCE
To the best of our knowledge, this study represents the first comprehensive analysis of antimicrobial resistance gene (AMRGs) expression in the fecal microbiota of Tibetan and Duroc pigs, employing an integrated metagenomic and metatranscriptomic approach. Our findings indicate a higher risk of AMRGs transmission in the feces of Duroc pigs compared to Tibetan pigs. Given the escalating antimicrobial resistance crisis, novel therapeutic interventions are imperative to mitigate gut colonization by pathogens and AMRGs. In this regard, we investigated the impact of fecal microbiota from Tibetan and Duroc pig sources on AMRGs excretion in Duroc Landrace Yorkshire (DLY) piglets’ feces following acute antibiotic exposure. Remarkably, only fecal microbiota sourced from Tibetan pigs exhibited a reduction in AMRGs excretion in DLY piglets’ feces. This underscores the significance of evaluating the presence of AMRGs within donor fecal microbiota for effective AMRGs decolonization strategies.
The prevalence of
optrA
-carrying
Enterococci
in the vaginal micro-ecology of pregnant women in late pregnancy
Authors: Xie Yanjun , Xu Fangyi , Dong Huali , Mao Jianfeng , Zhang Chuanling 
Published: November 2024

ABSTRACT

The colonization of
Enterococcus
in the female vagina leads to neonatal and pediatric enterococcal septicemia. Linezolid (LZD) is a kind of mainstream drug for treating multidrug-resistant Gram-positive infections.
OptrA
is the main LZD-resistance gene at
Enterococci
in human isolates. It is essential to explore the prevalence of
optrA
-carrying
Enterococcus
in vaginal secretions of late pregnant women and the drug resistance of
optrA
. From May to June 2023, this study recruited 340 volunteers in late pregnancy (35–40 weeks of pregnancy) to provide non-repetitive vaginal discharge samples. Luria-Bertani broth and florfenicol (10 µg/mL) were used to enrich bacteria.
Enterococci
was identified through time-of-flight mass spectrometry. Additionally, antimicrobial susceptibility, polymerase chain reaction, and next-generation sequencing assays were applied to this study. Fifty-four
optrA
-carrying
Enterococcus
strains were obtained, the proportion of the whole vagina of late pregnant women was 15.88% (54 out of 340), and
Enterococcus faecalis
account the highest proportion. All
optrA
-carrying
Enterococcus
were resistant to at least three drugs. Tetracycline, chloramphenicol, erythromycin, and LZD have higher bacterial resistance rates. Genetic environment analysis revealed that IS
1216E
,
fexA
, and
erm
(A) may synergistically exert multidrug resistance with
optrA
. It is necessary to strengthen the surveillance of
optrA
-carrying
Enterococcus
in pregnant women. This study provides scientific support for controlling hospital infections and managing antibiotic-resistant bacteria, and provides a scientific basis for rational clinical medication.

IMPORTANCE

The disruption of cervicovaginal microbiota homeostasis is considered a key factor in causing imbalance in the microenvironment, leading to inflammation, transmission of infections, and illness.
Enterococcus
is considered a major cause of healthcare-related infections globally. It has resistance to multiple antimicrobial drugs, which pose significant challenges for clinical treatment. Therefore, it is crucial to assess the prevalence of
optrA
-carrying
Enterococcus
in vaginal secretions of late pregnant women and the drug resistance of
optrA
. This study detected 15.88% of
optrA
-carried
Enterococci
in 340 pregnant women. Furthermore, we found that
optrA
-carrying
Enterococcus
strains are highly resistant to tetracycline, chloramphenicol, erythromycin, and Linezolid. Additionally, genetic environment analysis revealed that
IS1216E
,
fexA
, and
erm
(A) may synergistically exert multidrug resistance with
optrA
. This study provides scientific support for controlling hospital infections and managing antibiotic-resistant bacteria and provides a scientific basis for rational clinical medication.