bluuebunny/crossref_metadata_2025_split huggingface dataset:
MoRgs3 functions in intracellular reactive oxygen species perception-integrated cAMP signaling to promote appressorium formation in
Magnaporthe oryzae
Authors: Zhang Ruiming , Liu Xinyu , Xu Jiayun , Chen Chen , Tang Zhaoxuan , Wu Chengtong , Li Xinyue , Su Lei , Liu Muxing , Yang Leiyun , Li Gang , Zhang Haifeng , Wang Ping , Zhang Zhengguang 
Published: July 2024

ABSTRACT

Regulator of G-protein signaling (RGS) proteins exhibit GTPase-accelerating protein activities to govern G-protein function. In the rice blast fungus
Magnaporthe oryzae
, there is a family of at least eight RGS and RGS-like proteins (MoRgs1 to MoRgs8), each exhibiting distinct or shared functions in the growth, appressorium formation, and pathogenicity. MoRgs3 recently emerged as one of the crucial regulators that senses intracellular oxidation during appressorium formation. To explore this unique regulatory mechanism of MoRgs3, we identified the nucleoside diphosphate kinase MoNdk1 that interacts with MoRgs3. MoNdk1 phosphorylates MoRgs3 under induced intracellular reactive oxygen species levels, and MoRgs3 phosphorylation is required for appressorium formation and pathogenicity. In addition, we showed that MoRgs3 phosphorylation determines its interaction with MoCrn1, a coronin-like actin-binding protein homolog, which regulates MoRgs3 internalization. Finally, we provided evidence demonstrating that MoRgs3 functions in MoMagA-mediated cAMP signaling to regulate normal appressorium induction. By revealing a novel signal perception mechanism, our studies highlighted the complexity of regulation during the appressorium function and pathogenicity of the blast fungus.

IMPORTANCE

We report that MoRgs3 becomes phosphorylated in an oxidative intracellular environment during the appressorium formation stage. We found that this phosphorylation is carried out by MoNdk1, a nucleoside diphosphate kinase. In addition, this phosphorylation leads to a higher binding affinity between MoRgs3 and MoCrn1, a coronin-like actin-binding protein that was implicated in the endocytic transport of several other RGS proteins of
Magnaporthe oryzae
. We further found that the internalization of MoRgs3 is indispensable for its GTPase-activating protein function toward the Gα subunit MoMagA. Importantly, we characterized how such cellular regulatory events coincide with cAMP signaling-regulated appressorium formation and pathogenicity in the blast fungus. Our studies uncovered a novel intracellular reactive oxygen species signal-transducing mechanism in a model pathogenic fungus with important basic and applied implications.
Dependence of post-segregational killing mediated by Type II restriction–modification systems on the lifetime of restriction endonuclease effective activity
Authors: Kozlova Svetlana , Morozova Natalia , Ispolatov Yaroslav , Severinov Konstantin 
Published: July 2024

ABSTRACT

Plasmid-borne Type II restriction–modification (RM) systems mediate post-segregational killing (PSK). PSK is thought to be caused by the dilution of restriction and modification enzymes during cell division, resulting in accumulation of unmethylated DNA recognition sites and their cleavage by restriction endonucleases. PSK is the likely reason for stabilization of plasmids carrying RM systems in the absence of selection for plasmid maintenance. In this study, we developed a CRISPR interference-based method to eliminate RM-carrying plasmids and study PSK-related phenomena with minimal perturbation to the
Escherichia coli
host. Plasmids carrying the EcoRV, Eco29kI, and EcoRI RM systems were highly stable, and their loss resulted in SOS response and PSK. In contrast, plasmids carrying the Esp1396I system were poorly stabilized; their loss led to a temporary cessation of growth, followed by full recovery. We demonstrate that this unusual behavior is due to a limited lifetime of the Esp1396I restriction endonuclease activity, which, upon Esp1396I plasmid loss, disappears approximately after two cycles of cell division, i.e., before unmethylated sites appear in significant numbers. Our results indicate that whenever PSK induced by a loss of RM systems, and, possibly, other toxin–antitoxin systems, is considered, the lifetimes of individual system components and the growth rate of host cells shall be taken in account. Mathematical modeling shows, that unlike the situation with classical toxin–antitoxin systems, RM system-mediated PSK is possible when the lifetimes of restriction endonuclease and methyltransferase activities are similar, as long as the toxic restriction endonuclease activity persists for more than two chromosome replication cycles.

IMPORTANCE

It is widely accepted that many Type II restriction–modification (RM) systems mediate post-segregational killing (PSK) if plasmids that encode them are lost. In this study, we harnessed an inducible CRISPR-Cas system to remove RM plasmids from
Escherichia coli
cells to study PSK while minimally perturbing cell physiology. We demonstrate that PSK depends on restriction endonuclease activity lifetime and is not observed when it is less than two replication cycles. We present a mathematical model that explains experimental data and shows that unlike the case of toxin–antitoxin-mediated PSK, the loss of an RM system induced PSK even when the RM enzymes have identical lifetimes.
The spliceosome impacts morphogenesis in the human fungal pathogen
Candida albicans
Authors: Lash Emma , Maufrais Corinne , Janbon Guilhem , Robbins Nicole , Herzel Lydia , Cowen Leah E. 
Published: July 2024

ABSTRACT

At human body temperature, the fungal pathogen
Candida albicans
can transition from yeast to filamentous morphologies in response to host-relevant cues. Additionally, elevated temperatures encountered during febrile episodes can independently induce
C. albicans
filamentation. However, the underlying genetic pathways governing this developmental transition in response to elevated temperatures remain largely unexplored. Here, we conducted a functional genomic screen to unravel the genetic mechanisms orchestrating
C. albicans
filamentation specifically in response to elevated temperature, implicating 45% of genes associated with the spliceosome or pre-mRNA splicing in this process. Employing RNA-Seq to elucidate the relationship between mRNA splicing and filamentation, we identified greater levels of intron retention in filaments compared to yeast, which correlated with reduced expression of the affected genes. Intriguingly, homozygous deletion of a gene encoding a spliceosome component important for filamentation (
PRP19
) caused even greater levels of intron retention compared with wild type and displayed globally dysregulated gene expression. This suggests that intron retention is a mechanism for fine-tuning gene expression during filamentation, with perturbations of the spliceosome exacerbating this process and blocking filamentation. Overall, this study unveils a novel biological process governing
C. albicans
filamentation, providing new insights into the complex regulation of this key virulence trait.

IMPORTANCE

Fungal pathogens such as
Candida albicans
can cause serious infections with high mortality rates in immunocompromised individuals. When
C. albicans
is grown at temperatures encountered during human febrile episodes, yeast cells undergo a transition to filamentous cells, and this process is key to its virulence. Here, we expanded our understanding of how
C. albicans
undergoes filamentation in response to elevated temperature and identified many genes involved in mRNA splicing that positively regulate filamentation. Through transcriptome analyses, we found that intron retention is a mechanism for fine-tuning gene expression in filaments, and perturbation of the spliceosome exacerbates intron retention and alters gene expression substantially, causing a block in filamentation. This work adds to the growing body of knowledge on the role of introns in fungi and provides new insights into the cellular processes that regulate a key virulence trait in
C. albicans
.
Immunological correlates of protection mediated by a whole organism,
Cryptococcus neoformans
, vaccine deficient in chitosan
Authors: Specht Charles A. , Wang Ruiying , Oliveira Lorena V. N. , Hester Maureen M. , Gomez Christina , Mou Zhongming , Carlson Diana , Lee Chrono K. , Hole Camaron R. , Lam Woei C. , Upadhya Rajendra , Lodge Jennifer K. , Levitz Stuart M. 
Published: July 2024

ABSTRACT

The global burden of infections due to the pathogenic fungus
Cryptococcus
is substantial in persons with low CD4
+
T-cell counts. Previously, we deleted three chitin deacetylase genes from
Cryptococcus neoformans
to create a chitosan-deficient, avirulent strain, designated as
cda1∆2∆3∆
, which, when used as a vaccine, protected mice from challenge with virulent
C. neoformans
strain KN99. Here, we explored the immunological basis for protection. Vaccine-mediated protection was maintained in mice lacking B cells or CD8
+
T cells. In contrast, protection was lost in mice lacking α/β T cells or CD4
+
T cells. Moreover, CD4
+
T cells from vaccinated mice conferred protection upon adoptive transfer to naive mice. Importantly, while monoclonal antibody-mediated depletion of CD4
+
T cells just prior to vaccination resulted in complete loss of protection, significant protection was retained in mice depleted of CD4
+
T cells after vaccination but prior to challenge. Vaccine-mediated protection was lost in mice genetically deficient in interferon-γ (IFNγ), tumor necrosis factor alpha (TNFα), or interleukin (IL)-23p19. A robust influx of leukocytes and IFNγ- and TNFα-expressing CD4
+
T cells was seen in the lungs of vaccinated and challenged mice. Finally, a higher level of IFNγ production by lung cells stimulated ex vivo correlated with lower fungal burden in the lungs. Thus, while B cells and CD8
+
T cells are dispensable, IFNγ and CD4
+
T cells have overlapping roles in generating protective immunity prior to
cda1∆2∆3∆
vaccination. However, once vaccinated, protection becomes less dependent on CD4
+
T cells, suggesting a strategy for vaccinating HIV
+
persons prior to loss of CD4
+
T cells.

IMPORTANCE

The fungus
Cryptococcus neoformans
is responsible for >100,000 deaths annually, mostly in persons with impaired CD4
+
T-cell function such as AIDS. There are no approved human vaccines. We previously created a genetically engineered avirulent strain of
C. neoformans
, designated as
cda1∆2∆3∆
. When used as a vaccine,
cda1∆2∆3∆
protects mice against a subsequent challenge with a virulent
C. neoformans
strain. Here, we defined components of the immune system responsible for vaccine-mediated protection. We found that while B cells and CD8
+
T cells were dispensible, protection was lost in mice genetically deficient in CD4
+
T cells and the cytokines IFNγ, TNFα, or IL-23. A robust influx of cytokine-producing CD4
+
T cells was seen in the lungs of vaccinated mice following infection. Importantly, protection was retained in mice depleted of CD4
+
T cells following vaccination, suggesting a strategy to protect persons who are at risk of future CD4
+
T-cell dysfunction.
Genomic sequences of
Mycobacterium smegmatis
A cluster phages LBerry, Pembroke, and Zolita
Authors: Berry Nathan E. , Cassford Marly S. , Agostino Colby J. , Dionne Ethan N. , Schmitt Olivia J. , Butela Kristen A. , Jacobs-Sera Deborah , DeGiorgis Joseph A. , Cornely Kathleen 
Published: July 2024

ABSTRACT

LBerry, Pembroke, and Zolita are newly isolated bacteriophages that infect
Mycobacterium smegmatis
mc²155. Based on gene content similarity, LBerry and Pembroke are assigned to cluster A3, and Zolita is assigned to cluster A5. LBerry and Pembroke are 99% identical to Anaysia and Caviar, and Zolita is 99% identical to SydNat.
The direct and indirect drivers shaping RNA viral communities in grassland soils
Authors: Wu Ruonan , Zimmerman Amy E. , Hofmockel Kirsten S. 
Published: July 2024

ABSTRACT

Recent studies have revealed diverse RNA viral communities in soils. Yet, how environmental factors influence soil RNA viruses remains largely unknown. Here, we recovered RNA viral communities from bulk metatranscriptomes sequenced from grassland soils managed for 5 years under multiple environmental conditions including water content, plant presence, cultivar type, and soil depth. More than half of the unique RNA viral contigs (64.6%) were assigned with putative hosts. About 74.7% of these classified RNA viral contigs are known as eukaryotic RNA viruses suggesting eukaryotic RNA viruses may outnumber prokaryotic RNA viruses by nearly three times in this grassland. Of the identified eukaryotic RNA viruses and the associated eukaryotic species, the most dominant taxa were
Mitoviridae
with an average relative abundance of 72.4%, and their natural hosts, Fungi with an average relative abundance of 56.6%. Network analysis and structural equation modeling support that soil water content, plant presence, and type of cultivar individually demonstrate a significant positive impact on eukaryotic RNA viral richness directly as well as indirectly on eukaryotic RNA viral abundance via influencing the co-existing eukaryotic members. A significant negative influence of soil depth on soil eukaryotic richness and abundance indirectly impacts soil eukaryotic RNA viral communities. These results provide new insights into the collective influence of multiple environmental and community factors that shape soil RNA viral communities and offer a structured perspective of how RNA virus diversity and ecology respond to environmental changes.

IMPORTANCE
Climate change has been reshaping the soil environment as well as the residing microbiome. This study provides field-relevant information on how environmental and community factors collectively shape soil RNA communities and contribute to ecological understanding of RNA viral survival under various environmental conditions and virus-host interactions in soil. This knowledge is critical for predicting the viral responses to climate change and the potential emergence of biothreats.
Species pool and soil properties in mangrove habitats influence the species-immigration process of diazotrophic communities across southern China
Authors: Liao Nengjian , Pan Lianghao , Zhao Huaxian , Yang Shu , Qin Xinyi , Huang Jiongqing , Li Xiaoli , Dong Ke , Shi Xiaofang , Hou Qinghua , Chen Qingxiang , Wang Pengbin , Jiang Gonglingxia , Li Nan 
Published: July 2024

ABSTRACT

Microbial immigration is an ecological process in natural environments; however, the ecological trade-off mechanisms that govern the balance between species extinction and migration are still lacking. In this study, we investigated the mechanisms underlying the migration of diazotrophic communities from soil to leaves across six natural mangrove habitats in southern China. The results showed that the diazotrophic alpha and beta diversity exhibited significant regional and locational variations. The diazotrophic species pool gradually increased from the leaves to nonrhizosphere soil at each site, exhibiting a vertical distribution pattern. Mantel test analyses suggested that climate factors, particularly mean annual temperature, significantly influenced the structure of the diazotrophic community. The diazotrophic community assembly was mainly governed by dispersal limitation in soil and root samples, whereas dispersal limitation and ecological drift were dominant in leaves. Partial least squares path modeling revealed that the species pool and soil properties, particularly the oxidation-reduction potential and pH, were closely linked to the species-immigration ratio of diazotrophic communities. Our study provides novel insights for understanding the ecological trait diversity patterns and spread pathways of functional microbial communities between below- and aboveground habitats in natural ecosystems.

IMPORTANCE

Environmental selection plays key roles in microbial transmission. In this study, we have provided a comprehensive framework to elucidate the driving patterns of the ecological trade-offs in diazotrophic communities across large-scale mangrove habitats. Our research revealed that
Bradyrhizobium japonicum
,
Marinobacterium lutimaris
, and
Agrobacterium tumefaciens
were more abundant in root-associated soil than in leaves by internal and external pathways. The nonrhizospheric and rhizospheric soil samples harbored the most core amplicon sequence variants, indicating that these dominant diazotrophs could adapt to broader ecological niches. Correlation analysis indicated that the diversities of the diazotrophic community were regulated by biotic and abiotic factors. Furthermore, this study found a lower species immigration ratio in the soil than in the leaves. Both species pool and soil properties regulate the species-immigration mechanisms of the diazotrophic community. These results suggest that substantial species immigration is a widespread ecological process, leading to alterations in local community diversity across diverse host environments.
Dietary L-arabinose-induced gut dysbiosis exacerbates
Salmonella
infection outcome
Authors: Yu Jingchen , Tang Huang , Zhou Ning , Wang Zuoqiang , Huang Wanqiu , Chen Yana , Wang Danni , Ni Jinjing , Lu Jie , Yao Yu-Feng 
Published: July 2024

ABSTRACT

The gut microbiota is essential for providing colonization resistance against pathogens. Dietary sugars markedly shift the composition of the intestinal microbiota and alter host susceptibility to enteric infections. Here, we demonstrate the effect of L-arabinose on bacterial infection by using a mouse infection model with
Salmonella enterica
serovar Typhimurium (
S
. Tm). In the presence of microbiota, L-arabinose induces a dramatic expansion of
Enterobacteriaceae
, thereby decreasing the microbiota diversity and causing more severe systemic infection. However, L-arabinose supplementation does not alter the disease progression of
Salmonella
infection in a microbiota-depleted mouse model. More importantly, short-term supplementation of L-arabinose fails to exert anti-diabetic effects in
Salmonella
-infected hyperglycemia mice and still promotes infection. Overall, our work reveals that a high intake of dietary L-arabinose supports a bloom of
Enterobacteriaceae
in
Salmonella
-infected gut, further accelerating the process of systemic infection.

IMPORTANCE

L-arabinose is a promising natural sweetener and food additive for the regulation of hyperglycemia. Since diabetic subjects are more susceptible to infections, the safety of dietary L-arabinose in diabetic patients experiencing infection remains a concern. Our findings reveal that L-arabinose exacerbates
Salmonella
infection outcome by inducing gut microbiota dysbiosis in mice. High dietary intake of L-arabinose may be deleterious for diabetic individuals undergoing infection.
Changes in the microbial community of semen exposed to different simulated forensic situations
Authors: Zheng Yangyang , Ye Linying , Du Jieyu , Huang Litao , Lun Miaoqiang , He Meiyun , Xiao Guichao , Du Weian , Liu Chao , Chen Ling 
Published: July 2024

ABSTRACT

Semen is one of the common body fluids in sexual crime cases. The current methods of semen identification have certain limitations, so it is necessary to search for other methods. In addition, there are few reports of microbiome changes in body fluids under simulated crime scenes. It is essential to further reveal the changes in semen microbiomes after exposure to various simulated crime scenes. Semen samples from eight volunteers were exposed in closed plastic bags, soil, indoor, cotton, polyester, and wool fabrics. A total of 68 samples (before and after exposure) were collected, detected by 16S rDNA sequencing, and analyzed for the microbiome signature. Finally, a random forest model was constructed for body fluid identification. After exposure, the relative abundance of
Pseudomonas
and
Rhodococcus
changed dramatically in almost all groups. In addition, the treatment with the closed plastic bags or soil groups had a greater impact on the semen microbiome. According to the Shannon indices, the alpha diversity of the closed plastic bags and soil groups was much lower than that of the other groups. Attention should be given to the above two scenes in practical work of forensic medicine. In this study, the accuracy of semen recognition was 100%. The exposed semen can still be correctly identified as semen based on its microbiota characteristics. In summary, semen microbiomes exposed to simulated crime scenes still have good application potential for body fluid identification.

IMPORTANCE
In this study, the microbiome changes of semen exposed to different environments were observed, and the exposed semen microbiome still has a good application potential in body fluid identification.
Candida
spp.: the burden of a microorganism in a microbiology department
Authors: Soriano-Martín Ana , Alonso Roberto , Machado Marina , Reigadas Elena , Muñoz Patricia , Bouza Emilio 
Published: July 2024

ABSTRACT

There is no precise information available on the entire workload of isolating a specific microorganism in a clinical microbiology laboratory, and the costs associated with it have not been specifically estimated. In this descriptive retrospective study conducted at the microbiology department of a general teaching hospital from January 2021 to December 2022, we assessed the workload associated with identifying
Candida
species in all types of clinical samples and patients. Costs were estimated from data obtained from the hospital’s finance department and microbiology laboratory cost records. In 2 years, 1,008,231 samples were processed at our microbiology department, of which 8,775 had one or more
Candida
spp. isolates (9,683 total isolates). Overall, 5,151 samples with
Candida
spp. were identified from 2,383 inpatients. We isolated
Candida
spp. from 515.3 samples/100,000 population/year and from 92 samples/1,000 hospital admissions/year. By sample type, 90.8% were superficial, mainly mucosal. Only 9.1%
Candida
spp. were isolated from deep, usually sterile, samples, being mostly from ordinarily sterile fluids.
Candida albicans
was the main species (58.5%) identified, followed by
C. parapsilosis
complex,
C. glabrata
,
C. tropicalis,
and
C. krusei
. In admitted patients, the incidences of samples with
Candida
spp. isolates were 302.7 samples/100,000 population/year and 54 samples/1,000 admissions/year. The average cost of isolating and identifying
Candida
spp. was estimated at 25€ per culture-positive sample. To our knowledge, this is the first attempt to gage the workload and costs of
Candida
spp. isolation at a hospital microbiology department. These data can help assess the burden and significance of
Candida
isolation at other institutions and also help design measures for streamlining.

IMPORTANCE
We believe that this work is of interest because at present, there is no really accurate information available on the total workload involved in isolating a specific microorganism in a clinical microbiology laboratory. The costs related to this have also not been described. We have described the unrestricted workload of Candida spp. in all types of samples for all types of species and patients. We believe that this information would be necessary to collect and share this information as well as to collect it in a standardized way to know the current situation of Candida spp. workload in all clinical microbiology laboratories.