bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electron microscopy mapping of the DNA-binding sites of monomeric, dimeric, and multimeric KSHV RTA protein
Authors: Calhoun Jayla C. , Damania Blossom , Griffith Jack D. , Costantini Lindsey M. 
Published: September 2023

ABSTRACTMolecular interactions between viral DNA and viral-encoded protein are a prerequisite for successful herpesvirus replication and production of new infectious virions. Here, we examined how the essential Kaposi’s sarcoma-associated herpesvirus (KSHV) protein, RTA (replication and transcription activator), binds to viral DNA using transmission electron microscopy (TEM). Previous studies using gel-based approaches to characterize RTA binding are important for studying the predominant form(s) of RTA within a population and identifying the DNA sequences that RTA binds with high affinity. However, using TEM, we were able to examine individual protein-DNA complexes and capture the various oligomeric states of RTA when bound to DNA. Hundreds of images of individual DNA and protein molecules were collected and then quantified to map the DNA-binding positions of RTA bound to the two KSHV lytic origins of replication encoded within the KSHV genome. The relative size of RTA or RTA bound to DNA was then compared to protein standards to determine whether RTA complexed with DNA was monomeric, dimeric, or formed larger oligomeric structures. We successfully analyzed a highly heterogeneous data set and identified new DNA-binding sites for RTA that included both high- and low-frequency-binding sites. TEM micrographs provide evidence that the majority of RTA analyzed forms dimers and high order multimers when bound to KSHV origin of replication DNA sequences. Broadly, our findings expand upon our understanding of the degree to which DNA-binding locations and protein conformation are heterogeneous and how protein monomers and dimers function differently with respect to DNA-binding location specificity.IMPORTANCEKaposi’s sarcoma-associated herpesvirus (KSHV) is a human herpesvirus associated with several human cancers, typically in patients with compromised immune systems. Herpesviruses establish lifelong infections in hosts in part due to the two phases of infection: the dormant and active phases. Effective antiviral treatments to prevent the production of new viruses are needed to treat KSHV. A detailed microscopy-based investigation of the molecular interactions between viral protein and viral DNA revealed how protein-protein interactions play a role in DNA-binding specificity. This analysis will lead to a more in-depth understanding of KSHV DNA replication and serve as the basis for anti-viral therapies that disrupt and prevent the protein-DNA interactions, thereby decreasing spread to new hosts.
Complete sequence of the closed circular extrachromosomal element (CERE) of
Naegleria australiensis
De Jonckheere (strain PP 397)
Authors: Nguyen Brian T. , Chapman Nora M. , Johnson Niklas , Stessman Holly A. F. , Tracy Steven , Drescher Kristen M. 
Published: September 2023

ABSTRACT

Ribosomal RNA is not encoded in chromosomal DNA in amoebae of the Naegleria genus but the rRNA genes are located on closed circular extrachromosomal ribosomal DNA (rDNA)-containing elements (CERE). In this report, we describe the sequence of the CERE of
Naegleria australiensis
De Jonckheere (strain PP397).
Annotation of Secretariat and Hydrus, two DJ cluster phages isolated on
Gordonia rubripertincta
Authors: Bland Jackson , Miller Sydney , Algarin-Martinez Elijah D. , Biggs Abbigail M. , Cavasini Maria E. D. , Chase Michael A. , Coleman Caitlyn , Correa Victoria , Danielson Don F. , Dean Wynter R. , French Joseph L. , Horne Mae E. , Macumber Breanna M. , Martini Francesca Kristal , Mazzei Sydney G. , McGarrah Coen E. E. , Odegaard Oslow , Parameswaran Indu S. , Quarterman Corrisa , Rand Taylor M. , Ruiz-Houston Kira M. , Sciacchitano Ava R. , Seidensticker Nina S. , Soltys Anna , Terron-Osorio Adrian E. , Todd Allyson L. , Wood Audrey R. , Ungrey Maxwell D. , Pollenz Richard S. 
Published: September 2023

ABSTRACT

Secretariat and Hydrus are phages grouped into the DJ cluster that were isolated on
Gordonia rubripertincta
NRRL B-16540. The phages have 75% nucleotide identity and share 73% gene content. Secretariat has a genome with 84 predicted genes, while Hydrus has 91 predicted genes and can also infect
Gordonia terrae
3612.
The origin and evolution of IncF33 plasmids based on large-scale data sets
Authors: Gao Guolong , He Wanyun , Jiao Yanxiang , Cai Zhongpeng , Lv Luchao , Liu Jian-Hua 
Published: September 2023

ABSTRACT

To comprehensively understand the formation and evolution of IncF33 plasmids, a global collection of whole-genome sequences of 863 strains positive for IncF33 plasmid replicons was analyzed. The results showed that the IncF33 plasmids were mainly identified in
Enterobacterales
, of which
Escherichia coli
(86.44%) was the dominant host, followed by
Salmonella
(8.57%) and
Klebsiella pneumoniae
(3.48%).
Salmonella
ST11 and
K. pneumoniae
ST11 were common and mostly from humans. IncF33 plasmids were found worldwide but prevalent in Chinese farm animals, predominantly carrying antibiotic resistance genes such as
bla
CTX-M-55
,
fosA3
,
bla
TEM-1B
,
rmtB
, and
floR
. Comparative genomics analysis of 103 complete IncF33 plasmid sequences showed highly similar backbones except for 16 lacking partial backbone fragments. Variable regions were diverse, containing various antibiotic resistance genes, insertion sequences, or other plasmid fragments. They can be roughly divided into two sublines based on the production of different CTX-M enzymes. Similar IncF33 plasmids from different countries were identified. Some early IncF33 plasmids lacked part of their leader regions, which showed over 99% homology with early F2:A-:B- plasmids, indicating that leader regions of IncF33 likely came from F2:A-:B- plasmids. In addition, IncF33 plasmids cointegrating with other types of plasmids to form new cointegrate plasmids are increasing, making them more efficient in their dissemination and persistence in
Enterobacterales
, which could pose a significant threat to global public health.

IMPORTANCE

Plasmids that capture multiple antibiotic resistance genes are spreading widely, leading to the emergence and prevalence of multidrug-resistant bacteria. IncF33 plasmids are a newly emerged plasmid type highly prevalent in animal-source
Enterobacterales
in China, and they are important vectors for transmitting several clinically important antibiotic resistance genes. The study revealed that the IncF33 plasmid is mainly prevalent in China animal-derived
Escherichia coli
and has the potential for cointegration and intercontinental dissemination. Therefore, it is crucial to enhance surveillance and control measures to limit the spread of IncF33 plasmids and their associated antibiotic resistance genes.
Gut microbiota of Pacific white shrimp (
Litopenaeus vannamei
) exhibits distinct responses to pathogenic and non-pathogenic
Vibrio parahaemolyticus
Authors: Chang Yi-Ting , Ko Hao-Ting , Wu Ping-Lun , Kumar Ramya , Wang Han-Ching , Lu Hsiao-Pei 
Published: September 2023

ABSTRACT

Acute hepatopancreatic necrosis disease (AHPND), a high-mortality-rate shrimp disease, is caused by specific
Vibrio parahaemolyticus
(Vp) strains with a plasmid encoding the PirAB
Vp
toxins. As a bacterial pathogen, the invasion of AHPND-causing Vp might impose pressure on commensal microbiota in the shrimp gut, while the relationship between the pathogenesis of AHPND and the dysbiosis of gut bacterial communities remains unclear. Here we explored the temporal changes of shrimp gut microbiota in response to AHPND-causing and non-AHPND-causing Vp strains, with the non-infected controls as a baseline of the shrimp gut microbiota. The diversity and composition of bacterial communities from 168 gut samples (covering three treatments at seven time points with eight individuals per set) were investigated using 16S rRNA gene metabarcoding with high-throughput sequencing. The results showed that (i) species diversity of gut bacterial communities declined in Vp-infected shrimp, independent of the strain pathogenicity; (ii) taxonomic compositions of gut bacterial communities were significantly different between shrimp infected by AHPND-causing and non-AHPND-causing Vp strains; (iii) short-term (within 6 hours) compositional shifts in the gut microbiota were found only in AHPND-causing Vp-infected shrimp; (iv) the gut microbiota of AHPND-causing Vp-infected shrimp was enriched with genera
Photobacterium
and
Vibrio
, with a decline in
Candidatus
Bacilliplasma; and (v) functional predictions suggested the loss of normal metabolism due to compositional shifts in the gut microbiota. Our work reveals distinct features of community dynamics in shrimp gut microbiota, associated with pathogenic versus non-pathogenic
Vibrio
infections, providing a new perspective of the pathogenesis of AHPND.

IMPORTANCE

Shrimp production is continually threatened by newly emerging diseases, such as AHPND, which is caused by specific Vp strains. Previous studies on the pathogenesis of AHPND have mainly focused on the histopathology and immune responses of the host. However, more attention needs to be paid to the gut microbiota, which acts as the first barrier to pathogen colonization. In this study, we revealed that shrimp gut microbiota responded differently to pathogenic and non-pathogenic Vp strains, with bacterial genera
Photobacterium
and
Vibrio
enriched in pathogenic Vp-infected shrimp, and
Candidatus
Bacilliplasma enriched in non-pathogenic Vp-infected shrimp. Moreover, functional predictions suggested that changes in taxonomic compositions would further affect normal metabolic functions, emphasizing the importance of sustaining an equilibrium in the gut microbiota. Several biomarkers associated with specific microbial taxa and functional pathways were identified in our data sets, which help predict the incidence of disease outcomes.
Effects of pruning on tea tree growth, tea quality, and rhizosphere soil microbial community
Authors: Zhang Qi , Zhang Ying , Wang Yuhua , Lin Shaoxiong , Chen Meihui , Cheng Pengyuan , Ye Jianghua , Miao Pengyao , Jia Xiaoli , Wang Haibin 
Published: September 2023

ABSTRACT

Pruning is an important agronomic measure in tea plantation management. This study analyzed the effects of pruning on tea tree growth, tea quality, rhizosphere soil physicochemical indexes, microbial communities, and metabolic pathways. The results showed that pruning was beneficial for promoting tea tree growth and increasing tea yield, but not for the synthesis and accumulation of quality-related compounds in tea leaves. After pruning, organic matter, available phosphorus content and catalase, acid phosphatase, and sucrase activities in rhizosphere soil were significantly higher than those in unpruned tea trees, while total phosphorus, total potassium, and available nitrogen content were significantly lower than those in unpruned tea trees. The results of microbial community analysis of tea rhizosphere soil showed that the key changed characteristic microorganisms after pruning were
Haliangium
,
Acidicaldus
,
Reyranella
,
Acidobacterium
,
Aquicella
, and
Granulicella
, and the key changed characteristic microbial metabolic pathways were ko00072, ko00473, ko00750, ko01055, ko00521, and ko02040. Furthermore, the results found that pruning promoted
Haliangium, Acidicaldus
, and
Reyranella
abundances, ko00072, ko00473, and ko00750, respectively, microbial metabolic pathways in tea trees rhizosphere soil, and reduced
Acidobacterium
,
Granulicella,
and
Aquicella
abundance
,
ko01055, ko00521, and ko02040, respectively, microbial metabolic pathways, thereby increasing the activities of soil catalase, acid phosphatase, and sucrase, improving soil organic matter decomposition efficiency and available phosphorus content, and promoting tea yield, but not synthesis and accumulation of quality-related compounds in tea leaves. This study provides an important theoretical reference for the management of agronomic measures in tea plantations.

IMPORTANCE
Pruning is an important agronomic measure in tea cultivation and management. We found that pruning was beneficial to increase tea yield, but it would reduce tea quality, especially the content of polyphenols, theanine, flavonoids, and free amino acids in tea leaves was reduced. The reason for this phenomenon was that pruning promotes the enrichment of special functional microorganisms and the enhancement of special metabolic pathways in the soil, leading to changes in the nutrient cycle in the soil.
Proteasome inhibition as a therapeutic target for the fungal pathogen
Cryptococcus neoformans
Authors: Caza Mélissa , Santos Daniel Assis , Burden Elizabeth , Brisland Anna , Hu Guanggan , Kronstad James W. 
Published: September 2023

ABSTRACT

The current therapeutic challenges for treating fungal diseases demand new approaches and new drugs. A promising strategy involves combination therapy with agents of distinct mechanisms of action to increase fungicidal activity and limit the impact of mutations leading to resistance. In this study, we evaluated the antifungal potential of bortezomib by examining the inhibition of proteasome activity, cell proliferation, and capsule production by
Cryptococcus neoformans
, the causative agent of fungal meningoencephalitis. Chemical genetic screens with collections of deletion mutants identified potential druggable targets for combination therapy with bortezomib. In vitro assays of combinations of bortezomib with flucytosine, chlorpromazine, bafilomycin A1, copper sulfate, or hydroxyurea revealed antifungal effects against
C. neoformans
. Furthermore, combination treatment with bortezomib and flucytosine in a murine inhalation model of cryptococcosis resulted in the improvement of neurological functions and reduced fungal replication and dissemination, leading to a delay in disease progression. This study therefore highlights the utility of chemical genetic screens to identify new therapeutic approaches as well as the antifungal potential of proteasome inhibition.

IMPORTANCE

Fungal diseases of humans are difficult to treat, and there is a clear need for additional antifungal drugs, better diagnostics, effective vaccines, and new approaches to deal with emerging drug resistance. Fungi are challenging to control because they share many common biochemical functions with their mammalian hosts and it is therefore difficult to identify fungal-specific targets for drug development. One approach is to employ existing antifungal drugs in combination with agents that target common cellular processes at levels that are (ideally) not toxic for the host. We pursued this approach in this study by examining the potential of the clinically approved proteasome inhibitor bortezomib to influence the proliferation and virulence of
Cryptococcus neoformans
. We found that the combination of bortezomib with the anti-cryptococcal drug flucytosine improved the survival of infected mice, thus demonstrating the potential of this strategy for antifungal therapy.
Exploring the genetic background of the botulism neurotoxin BoNT/B2 in Spain
Authors: Valdezate Sylvia , Carrasco Gema , Medina María J. , Garrido Noelia , del Pino Silvia , Valiente Monica , Pallarés María P. , Villalon Pilar 
Published: September 2023

ABSTRACT

To determine whether the neurotoxin BoNT/B2 causing botulism in Spain is clonal, the genetic diversity and phylogenetic relationships of
Clostridium botulinum
from food-borne episodes and infant cases of the condition were explored. The botulinum toxin gene (
bont
) subtype, the variable region of the flagellin gene (
fla
VR), and a seven-gene multi-locus sequence type were examined by sequencing 37 BoNT-positive cultures obtained over the period 2010 to 2022. Out of 37 botulism events, 16 food-borne episodes and 16 infant cases were associated with
bont/b
2. Eight
bont/b
2 alleles were detected [nucleotide distance range 0.0259–0.415%, Hunter and Gaston discrimination index (HGDI) 0.71]. The most common
bont/b
2 allele corresponded to that of strain Prevot 25 NCASE and its single and double locus variations (87.5%). Four known
fla
VR types were identified (HGDI 0.79), along with one previously unknown (
fla
VR-15). Sixteen sequence types (STs) (HGDI 0.89) were recorded including seven new STs (ST164–ST170; 10 new alleles) and five new STs (ST171–ST175; with new allele combinations) were also noted. Correlations among some STs and
fla
VR types were seen. Overall, the present results show that the combined analysis of
bont/b
2-
fla
VR-ST at the nucleotide level could be used to track botulism events in Spain. The neurotoxin BoNT/B2 has largely been responsible for human botulism in Spain. The polymorphism analysis of
bont/b2
,
fla
VR typing, and sequence type determinations, revealed a wide variety of clones to be responsible for human botulism, ruling out a common source of acquisition.

IMPORTANCE

Botulism, a potentially fatal disease, is classically characterized by a symmetrical descending flaccid paralysis, which if left untreated can lead to respiratory failure and death. Botulinum neurotoxin (BoNT), produced by certain species of Clostridium, is the most potent biological toxin known, and the direct cause of botulism. This study characterizes the acquisition in Spain of two forms of botulism, i.e., food-borne and infant botulism, which are largely caused by the main neurotoxin BoNT/B2. Polymorphism analysis of the bont/b2 gene, typing of the flagellin variable region sequence (flaVR), and multilocus sequence typing, were used to explore the genetic background of
Clostridium botulinum
group I. To our knowledge, this is the first phylogenetic and typing study of botulism undertaken in Spain.
Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques
Authors: Roche Christina E. , Montague Michael J. , Wang JiCi , Dickey Allison N. , Ruiz-Lambides Angelina , Brent Lauren J. N. , Platt Michael L. , Horvath Julie E. 
Published: September 2023

ABSTRACT
While skin microbes are known to mediate human health and disease, there has been minimal research on the interactions between skin microbiota, social behavior, and year-to-year effects in non-human primates—important animal models for translational biomedical research. To examine these relationships, we analyzed skin microbes from 78 rhesus macaques living on Cayo Santiago Island, Puerto Rico. We considered age, sex, and social group membership, and characterized social behavior by assessing dominance rank and patterns of grooming as compared to nonsocial behaviors. To measure the effects of a shifting environment, we sampled skin microbiota (based on sequence analysis of the 16S rRNA V4 region) and assessed weather across sampling periods between 2013 and 2015. We hypothesized that, first, monkeys with similar social behavior and/or in the same social group would possess similar skin microbial composition due, in part, to physical contact, and, second, microbial diversity would differ across sampling periods. We found significant phylum-level differences between social groups in the core microbiome as well as an association between total grooming rates and alpha diversity in the complete microbiome, but no association between microbial diversity and measures of rank or other nonsocial behaviors. We also identified alpha and beta diversity differences in microbiota and differential taxa abundance across two sampling periods. Our findings indicate that social dynamics interact with yearly environmental changes to shape the skin microbiota in rhesus macaques, with potential implications for understanding the factors affecting the microbiome in humans, which share many biological and social characteristics with these animals.

IMPORTANCE
Primate studies are valuable for translational and evolutionary insights into the human microbiome. The majority of primate microbiome studies focus on the gut, so less is known about the factors impacting the microbes on skin and how their links affect health and behavior. Here, we probe the impact of social interactions and the yearly environmental changes on food-provisioned, free-ranging monkeys living on a small island. We expected animals that lived together and groomed each other would have more similar microbes on their skin, but surprisingly found that the external environment was a stronger influence on skin microbiome composition. These findings have implications for our understanding of the human skin microbiome, including potential manipulations to improve health and treat disease.
Structural biology and functional features of phage-derived depolymerase Depo32 on
Klebsiella pneumoniae
with K2 serotype capsular polysaccharides
Authors: Cai Ruopeng , Ren Zhuolu , Zhao Rihong , Lu Yan , Wang Xinwu , Guo Zhimin , Song Jinming , Xiang Wentao , Du Rui , Zhang Xiaokang , Han Wenyu , Ru Heng , Gu Jingmin 
Published: September 2023

ABSTRACT

Hypervirulent
Klebsiella pneumoniae
with capsular polysaccharides (CPSs) causes severe nosocomial- and community-acquired infections. Phage-derived depolymerases can degrade CPSs from
K. pneumoniae
to attenuate bacterial virulence, but their antimicrobial mechanisms and clinical potential are not well understood. In the present study,
Klebsiella
phage GH-K3-derived depolymerase Depo32 (encoded by gene
gp32
) was identified to exhibit high efficiency in specifically degrading the CPSs of K2 serotype
K. pneumoniae
. The cryo-electron microscopy structure of trimeric Depo32 at a resolution up to 2.32 Å revealed potential catalytic centers in the cleft of each of the two adjacent subunits.
K. pneumoniae
subjected to Depo32 became more sensitive to phagocytosis by RAW264.7 cells and activated the cells by the mitogen-activated protein kinase signaling pathway. In addition, intranasal inoculation with Depo32 (a single dose of 200 µg, 20 µg daily for 3 days, or in combination with gentamicin) rescued all C57BL/6J mice infected with a lethal dose of
K. pneumoniae
K7 without interference from its neutralizing antibody. In summary, this work elaborates on the mechanism by which Depo32 targets the degradation of K2 serotype CPSs and its potential as an antivirulence agent.

IMPORTANCE

Depolymerases specific to more than 20 serotypes of
Klebsiella
spp. have been identified, but most studies only evaluated the single-dose treatment of depolymerases with relatively simple clinical evaluation indices and did not reveal the anti-infection mechanism of these depolymerases in depth. On the basis of determining the biological characteristics, the structure of Depo32 was analyzed by cryo-electron microscopy, and the potential active center was further identified. In addition, the effects of Depo32 on macrophage phagocytosis, signaling pathway activation, and serum killing were revealed, and the efficacy of the depolymerase (single treatment, multiple treatments, or in combination with gentamicin) against acute pneumonia caused by
Klebsiella pneumoniae
was evaluated. Moreover, the roles of the active sites of Depo32 were also elucidated in the
in vitro
and
in vivo
studies. Therefore, through structural biology, cell biology, and
in vivo
experiments, this study demonstrated the mechanism by which Depo32 targets K2 serotype
K
.
pneumoniae
infection.