-
Genetic evidence for a regulated cysteine protease catalytic triad in LegA7, a Legionella pneumophila protein that impinges on a stress response pathway bioRxiv. Microbiol. Pub Date : 2024-03-18 Dar Hershkovitz, Emy J. Chen, Alexander W Ensminger, Aisling S. Dugan, Alex C. Joyce, Gil Segal, Ralph R Isberg
Legionella pneumophila grows within membrane-bound vacuoles in phylogenetically diverse hosts. Intracellular growth requires the function of the Icm/Dot type-IVb secretion system, which translocates more than 300 proteins into host cells. A screen was performed to identify L. pneumophila proteins that stimulate MAPK activation, using Icm/Dot translocated proteins ectopically expressed in mammalian
-
Selective enrichment of Methylococcaceae versus Methylocystaceae methanotrophs via control of methane feeding scheme bioRxiv. Microbiol. Pub Date : 2024-03-18 Ju Yong Lee, Munjeong Choi, Min Joon Song, Daehyun Daniel Kim, Taeho Yun, Jin Chang, Adrian Ho, Jaewook Myung, Sukhwan Yoon
Methanotrophs are crucial in keeping environmental CH4 emissions in check. However, how different groups of methanotrophs contribute to this important role in different environmental settings remain ambiguous. Here, in a simplified laboratory setting of well-mixed batch reactors fed continuous flow of CH4-containing gas, methanotrophic microbiomes were enriched from paddy soils under six different
-
Isolate-anchored comparisons reveal evolutionary and functional differentiation across SAR86 marine bacteria bioRxiv. Microbiol. Pub Date : 2024-03-18 Oscar Ramfelt, Kelle C. Freel, Sarah J. Tucker, Olivia D. Nigro, Michael S. Rappé
SAR86 is one of the most abundant groups of bacteria in the global surface ocean. However, since its discovery over 30 years ago, it has remained recalcitrant to isolation and many details regarding this group are still unknown. Here we report the cellular characteristics from the first SAR86 isolate brought into culture, Candidatus Magnimaribacter mokuoloeensis strain HIMB1674, and use its closed
-
Myosin A and F-Actin play a critical role in mitochondrial dynamics and inheritance in Toxoplasma gondii bioRxiv. Microbiol. Pub Date : 2024-03-18 Rodolpho Ornitz Oliveira Souza, Chunlin Yang, Gustavo Arrizabalaga
The single mitochondrion of the obligate intracellular parasite Toxoplasma gondii is highly dynamic. Toxoplasma's mitochondrion changes morphology as the parasite moves from the intracellular to the extracellular environment and during division. Toxoplasma's mitochondrial dynamic is dependent on an outer mitochondrion membrane-associated protein LMF1 and its interaction with IMC10, a protein localized
-
Tobacco Smoke Exposure is Characterized by a Distinct Nasal Rhinotype in a Pediatric Population bioRxiv. Microbiol. Pub Date : 2024-03-18 Hilary Monaco, Cordelia Elaiho, Bian Liu, Tiffany Chan, Adam Cantor, Joseph Michael Collaco, Sharon McGrath-Morrow, Karen Wilson, Jose C Clemente
Secondhand tobacco smoke exposure (TSE) increases susceptibility to respiratory diseases, but the mechanisms of action are poorly understood. Here we study the effect of TSE in the nasal microbiome of children, and to evaluate whether such effect is dose-dependent with measured levels of cotinine in saliva and urine. This study was performed at the Mount Sinai Kravis Childrens Hospital (New York, NY)
-
Mutational analysis of the F plasmid partitioning protein ParA reveals novel residues required for oligomerisation and plasmid maintenance bioRxiv. Microbiol. Pub Date : 2024-03-18 Nivedita Mitra, Dipika Mishra, Irene Aniyan Puthethu, RAMANUJAM SRINIVASAN
Mobile genetic elements such as plasmids play a crucial role in the emergence of antimicrobial resistance. Hence, plasmid maintenance proteins like ParA of the Walker A type cytoskeletal ATPases/ ParA superfamily are potential targets for novel antibiotics. Plasmid partitioning by ParA relies upon ATP-dependent dimerisation and formation of chemophoretic gradients of ParA-ATP on bacterial nucleoids
-
De novo PADI4-mediated citrullination of histone H3 stimulates HIV-1 transcription bioRxiv. Microbiol. Pub Date : 2024-03-18 Luca Love, Bianca B Jutte, Birgitta Lindqvist, Naomi Ann Thomas, Oscar Kieri, Piotr Nowak, J. Peter Svensson
HIV-1 infection establishes a reservoir of long-lived cells with integrated proviral DNA that can persist despite antiretroviral therapy (ART). The mechanisms governing the transcriptional regulation of the provirus are complex and incompletely understood. Here, we investigated the role of histone H3 citrullination, a post-translational modification catalyzed by protein-arginine deiminase type-4 (PADI4)
-
Viral challenges and adaptations between Central Arctic Ocean and atmosphere bioRxiv. Microbiol. Pub Date : 2024-03-17 Janina Rahlff, George Westmeijer, Julia Weissenbach, Alfred Antson, Karin Holmfeldt
Aquatic viruses act as key players in shaping microbial communities. In polar environments, they face significant challenges like limited host availability and harsh conditions. However, due to restricted ecosystem accessibility, our understanding of viral diversity, abundance, adaptations, and host interactions remains limited. To fill this knowledge gap, we studied viruses from atmosphere-close aquatic
-
Suppressive effects of oroxylin A on intracellular proliferation of Toxoplasma gondii via host cell ERK phosphorylation inhibition bioRxiv. Microbiol. Pub Date : 2024-03-17 Ziyue Z Zhang, Kazumi Norose, Noriko Shinjyo, Xiaoxia X Lin, Akiko Suganami, Yutaka Tamura, Hirokazu Sakamoto, Kenji Hikosaka
Toxoplasma gondii poses a significant threat to immunocompromised patients, resulting in high mortality rates. Considering the side effects of anti-Toxoplasma drugs, we focused on a potential candidate, oroxylin A (OA), a common component extracted from Astragalus membranaceus and Scutellaria baicalensis which suppressed the growth of T. gondii in vitro and in vivo. Our result demonstrated that OA
-
The dynamin-related protein Dyn2 is essential for both apicoplast and mitochondrial fission in Plasmodium falciparum bioRxiv. Microbiol. Pub Date : 2024-03-17 Alexander A. Morano, Wei Xu, Neeta Shadija, Jeffrey D Dvorin, Hangjun Ke
Dynamins, or dynamin-related proteins (DRPs), are large mechano-sensitive GTPases mediating membrane dynamics or organellar fission/fusion events. Plasmodium falciparum encodes three dynamin-like proteins whose functions are poorly understood. Here, we demonstrate that PfDyn2 mediates both apicoplast and mitochondrial fission. Using super-resolution and ultrastructure expansion microscopy, we show
-
Revealing Gene Expression Heterogeneity in a Clonal Population of Tetrahymena thermophila through Single-Cell RNA Sequencing bioRxiv. Microbiol. Pub Date : 2024-03-17 Hiroki Kojima, Akiko Kashiwagi, Takashi Ikegami
We performed single-cell RNA sequencing (scRNA-seq) on a population of 5,000 Tetrahymena thermophila, using the 10x Genomics 3' gene expression analysis, to investigate gene expression variability within this clonal population. Initially, we estimated the 3ʹ-untranslated regions (3' UTRs), which were absent in existing annotation files but are crucial for the 10x Genomics 3' gene expression analysis
-
Multiplexed screen identifies a Pseudomonas aeruginosa-specific small molecule targeting the outer membrane protein OprH and its interaction with LPS bioRxiv. Microbiol. Pub Date : 2024-03-16 Thulasi Warrier, Bradley E Poulsen, Sulyman Barkho, Josephine Bagnall, Keith P Romano, Tiantian White, Xiao Yu, Tomohiko Kawate, Phuong H Nguyen, Kyra Raines, Kristina Ferrara, Aaron Golas, Michael Fitzgerald, Andras Boeszoermenyi, Virendar Kaushik, Michael Serrano-Wu, Noam Shoresh, Deborah T Hung
The surge of antimicrobial resistance threatens efficacy of current antibiotics, particularly against Pseudomonas aeruginosa, a highly resistant gram-negative pathogen. The asymmetric outer membrane (OM) of P. aeruginosa combined with its array of efflux pumps provide a barrier to xenobiotic accumulation, thus making antibiotic discovery challenging. We adapted PROSPECT1, a target-based, whole-cell
-
Bottlenecks in the Implementation of Genome Scale Metabolic Model Based Designs for Bioproduction from Aromatic Carbon Sources bioRxiv. Microbiol. Pub Date : 2024-03-16 Deepanwita Banerjee, Javier Menasalvas, Yan Chen, Jennifer W Gin, Edward EK Baidoo, Christopher J Petzold, Thomas Eng, Aindrila Mukhopadhyay
Genome scale metabolic models (GSMM) are commonly used to identify gene deletion sets that result in growth coupling, pairing product formation with substrate utilization. While such approaches can improve strain performance beyond levels typically accessible using targeted strain engineering approaches, sustainable feedstocks often pose a challenge for GSMM-based methods due to incomplete underlying
-
Rapid evolution of Klebsiella pneumoniae biofilms in vitro delineates adaptive changes selected during infection bioRxiv. Microbiol. Pub Date : 2024-03-16 Greta Zaborskytė, Patrícia Coelho, Marie Wrande, Linus Sandegren
Biofilm formation facilitates infection by the opportunistic pathogen Klebsiella pneumoniae, primarily through indwelling medical devices. Here, we address how K. pneumoniae can increase its biofilm capacity by experimental evolution of surface-attached biofilms to mimic catheter-associated infections. We observed rapid convergent evolution that altered or abolished capsule, modified the fimbrial adhesin
-
Wildlife as a sentinel for pathogen introduction in non-endemic areas: Is Leishmania tropica circulating in wildlife in Spain? bioRxiv. Microbiol. Pub Date : 2024-03-16 Iris Azami-Conesa, Pablo Matas Mendez, Paula Perez-Moreno, Javier Carrion, Jose Maria Alunda, Marta Mateo Barrientos, Maria Teresa Gomez_Munoz
Background: Leishmaniasis is a global arthropod-borne zoonotic disease of chronic course and cutaneous, mucocutaneous, and visceral clinical manifestations. In the Iberian Peninsula, only Leishmania infantum has been reported, although other species of Leishmania, such as L. tropica and L. major, are present in surrounding countries. Aim: The aim of this work is to analyse the occurrence of Leishmania
-
Macrophage-induced reduction of bacteriophage density limits the efficacy of in vivo pulmonary phage therapy bioRxiv. Microbiol. Pub Date : 2024-03-16 Sophia Zborowsky, Jeremy Seurat, Quentin Balacheff, Chau Nguyen Ngoc Minh, Marie Titecat, Emma Evrard, Rogelio A Rodriguez-Gonzalez, Jacopo Marchi, Joshua S Weitz, Laurent Debarbieux
The rise of antimicrobial resistance has led to renewed interest in evaluating phage therapy. In murine models highly effective treatment of acute pneumonia caused by Pseudomonas aeruginosa relies on the synergistic antibacterial activity of bacteriophages with neutrophils. Here, we show that depletion of alveolar macrophages (AM) shortens the survival of mice without boosting the P. aeruginosa load
-
Global Release of Translational Repression Across Plasmodiums Host-to-Vector Transmission Event bioRxiv. Microbiol. Pub Date : 2024-03-16 Kelly T. Rios, James P. McGee, Aswathy Sebastian, Robert L. Moritz, Marina Feric, Sabrina Absalon, Kristian E. Swearingen, Scott E. Lindner
Malaria parasites must be able to respond quickly to changes in their environment, including during their transmission between mammalian hosts and mosquito vectors. Therefore, before transmission, female gametocytes proactively produce and translationally repress mRNAs that encode essential proteins that the zygote requires to establish a new infection. This essential regulatory control requires the
-
First insights of the Danube sturgeon (Acipenser gueldenstaedtii) skin adherent microbiota bioRxiv. Microbiol. Pub Date : 2024-03-16 Razvan Matache, Gyorgy Deak, Abdulhusein Jawdhari, Isabela Sadica, Cristian-Emilian Pop, Sergiu Fendrihan, Nicolai Craciun
This study assesses the microbial composition associated with the skin of Acipenser gueldenstaedtii, emphasizing species that are adherent. Various growth media were employed to cultivate samples collected from a group of 12 sturgeons from the same batch, revealing a diverse and atypical bacterial population. Notably, Ralstonia pickettii is documented here for the first time, as there have been no
-
N-acyl homoserine lactone signaling modulates bacterial community associated with human dental plaque bioRxiv. Microbiol. Pub Date : 2024-03-15 Rakesh Sikdar, Mai V Beauclaire, Bruno P Lima, Mark C Herzberg, Mikael H Elias
N-acyl homoserine lactones (AHLs) are small diffusible signaling molecules that mediate a cell density-dependent bacterial communication system known as quorum sensing (QS). AHL-mediated QS regulates gene expression to control many critical bacterial behaviors including biofilm formation, pathogenicity, and antimicrobial resistance. Dental plaque is a complex multispecies oral biofilm formed by successive
-
Advancing microbial isolation: The impact of leaf mold extract agar on soil samples bioRxiv. Microbiol. Pub Date : 2024-03-15 Atsushi Miyashita, Kazuhiro Mikami, Masaki Ishii, Masanobu Miyauchi, Fumiaki Tabuchi
In this study, we developed a new agar medium using leaf mold extract and evaluated its microbial cultivation performance with soil samples. As a control for performance evaluation, the general-purpose nutrient medium YME agar was used. For YME agar, isolated microbes were confirmed to belong mainly to the Bacillus genus through 16S rRNA gene sequencing. In contrast, for the leaf mold agar, bacteria
-
Clostridium innocuum, an opportunistic gut pathogen, inactivates host gut progesterone and arrests ovarian follicular development bioRxiv. Microbiol. Pub Date : 2024-03-15 Mei-Jou Chen, Chia-Hung Chou, Tsun-Hsien Hsiao, Tien-Yu Wu, Chi-Ying Li, Yi-Lung Chen, Kuang-Han Chao, Tzong-Huei Lee, Ronnie Gicana, Chao-Jen Shih, Guo-Jie Brandon-Mong, Yi-Li Lai, Po-Ting Li, Yu-Lin Tseng, Po-Hsiang Wang, Yin-Ru Chiang
Levels of progesterone, an endogenous female hormone, increase after ovulation; progesterone is crucial in the luteal phase to maintain successful pregnancy and prevent early miscarriage. Both endogenous and exogenous progesterone are recycled between the liver and gut; thus, the gut microbiota regulate host progesterone levels by inhibiting enterohepatic progesterone circulation. Our data indicated
-
The Toxoplasma gondii mitochondrial transporter ABCB7 is essential for cytosolic iron-sulfur cluster biogenesis and protein translation bioRxiv. Microbiol. Pub Date : 2024-03-15 Andrew E Maclean, Megan A Sloan, Eléa A Renaud, Vincent Demolombe, Sébastien Besteiro, Lilach Sheiner
Iron-sulfur (Fe-S) clusters are ubiquitous inorganic cofactors required for numerous essential cellular pathways. Since they cannot be scavenged from the environment, Fe-S clusters are synthesised de novo in cellular compartments such as the apicoplast, mitochondrion and cytosol. The cytosolic Fe-S cluster biosynthesis pathway relies on transport of an intermediate from the mitochondrial pathway. An
-
Common soil history is more important than plant history for arbuscular mycorrhizal community assembly in an experimental grassland diversity gradient bioRxiv. Microbiol. Pub Date : 2024-03-15 Cynthia Albracht, Marcel Dominik Solbach, Justus Hennecke, Leonardo Bassi, Geert Roelof van der Ploeg, Nico Eisenhauer, Alexandra Weigelt, Francois Buscot, Anna Heintz-Buschart
The relationship between biodiversity and ecosystem functioning strengthens with ecosystem age. However, the interplay between the plant diversity - ecosystem functioning relationship and Glomeromycotinian arbuscular mycorrhizal fungi (AMF) community assembly has not yet been scrutinized in this context, despite AMF's role in plant survival and niche exploration. We study the development of AMF communities
-
A functional circadian clock regulates composition and daily bacterial load of the gut microbiome in Drosophila melanogaster bioRxiv. Microbiol. Pub Date : 2024-03-15 Matteo Battistolli, Irene Varponi, Ottavia Romoli, Federica Sandrelli
While Drosophila melanogaster serves as a crucial model for investigating both the circadian clock and gut microbiome, our understanding of their relationship in this organism is still limited. Recent analyses suggested that the Drosophila gut microbiome modulates the host circadian transcriptome to minimize rapid oscillations in response to changing environments. To delve deeper into the potential
-
Bradyrhizobium and the soybean rhizosphere: Species level bacterial population dynamics in established soybean fields, rhizosphere and nodules. bioRxiv. Microbiol. Pub Date : 2024-03-15 Sukhvir Kaur Sarao, Vincent Boothe, Bikram Kumar Das, Jose L Gonzalez Hernandez, Volker S Brozel
Bradyrhizobium fixes nitrogen symbiotically with soybean and is an agriculturally significant bacterium. Much is known about the Bradyrhizobium species that nodulate soybeans. Conversely, prevalence of Bradyrhizobium in soil and the rhizosphere is known only to the genus level as culture independent approaches have provided only partial 16S rRNA gene sequences, so that nodulating and non-nodulating
-
Comprehensive non-black box classification of highly correlated ecological time series pairs containing many zeros: the case of gut microbiome of mice bioRxiv. Microbiol. Pub Date : 2024-03-15 Rie Maskawa, Hideki Takayasu, Tanzila Islam, Lena Takayasu, Rina Kurokawa, Hiroaki Masuoka, Wataru Suda, Misako Takayasu
We developed a new data analysis method, named Coexistence–Exclusion–Synchronization–Antisynchronization (CESA), to reveal statistically significant correlations from a set of integer compositional abundance time series of Operational Taxonomic Unit (OTU) data of mouse gut microbiota. First, time series are transformed to 0 (absence) and 1 (presence), and statistical tests are applied to extract significant
-
Epidemiological, Serological, and Virological Analysis of an Outbreak of Elephant Hemorrhagic Disease in Switzerland bioRxiv. Microbiol. Pub Date : 2024-03-15 Mathias Ackermann, Jakub Kubacki, Sarah Heaggans-Ebbeson, Gary S. Hayward, Julia Lechmann
Elephant hemorrhagic disease (EHD), caused by several Elephant endotheliotropic herpesviruses (EEHV), represents a frequently lethal syndrome, affecting both captive and free-living elephants. In summer 2022, three young Asian elephants (Elephas maximus) succumbed to EHD in a zoo in Switzerland, despite of considerable preventive efforts and early detection of EEHV1A viremia. In this communication
-
ONE HEALTH APPROACH ON SARS-COV-2 - USING SHEEP AS SENTINEL ANIMALS TO INCREASE FUTURE PANDEMIC PREPAREDNESS - a pilot study bioRxiv. Microbiol. Pub Date : 2024-03-15 Milena Samojlovic, Joao Mesquita, Sergio Santos-Silva, Malin Neptin, Joakim Esbjornsson
Coronaviruses are a family of viruses that can infect a number of species of birds and mammals with great zoonotic potential to cross species barriers and cause spill-over events. SARS-CoV-2 has been shown to cause clinical and inapparent disease and mortality in several animals cohabitating with humans. Sheep are also susceptible to SARS-CoV-2 and have potential to harbor and spread the virus, as
-
An expanded genetic toolkit for inducible expression and targeted gene silencing in Rickettsia parkeri bioRxiv. Microbiol. Pub Date : 2024-03-15 Jon McGinn, Annie Wen, Desmond L Edwards, David M Brinkley, Rebecca L Lamason
Pathogenic species within the Rickettsia genus are transmitted to humans through arthropod vectors and cause a spectrum of diseases ranging from mild to life-threatening. Despite rickettsiae posing an emerging global health risk, the genetic requirements of their infectious life cycles remain poorly understood. A major hurdle toward building this understanding has been the lack of efficient tools for
-
Differential Patterns of Cross-Protection against Antigenically Distinct Variants in Small Animal Models of SARS-CoV-2 Infection bioRxiv. Microbiol. Pub Date : 2024-03-15 Prabhuanand Selvaraj, Charles B Stauft, Shufeng Liu, Kotou Sangare, Tony T Wang
Continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will likely force more future updates of vaccine composition. Based on a series of studies carried out in human ACE2 transgenic mice (K18-hACE2) and Syrian hamsters, we show that immunity at the respiratory tract, acquired through either previous infection or vaccination with an in-house live attenuate virus, offers
-
Rust Fungus Red Data List and Census Catalogue for Wales bioRxiv. Microbiol. Pub Date : 2024-03-15 Ray Gareth Woods, R Nigel Stringer, Debbie A Evans, Arthur O Chater
The rust fungi are a group of specialised plant pathogens. Conserving them seems to fly in the face of reason. Yet as our population grows and food supplies become more precarious, controlling pathogens of crop plants becomes more imperative. Breeding resistance genes into such plants has proved to be the most cost effective solution. Such resistance genes evolve only in plants challenged by pathogens
-
Unveiling genome plasticity and a novel phage in Mycoplasma felis: Genomic investigations of four feline isolates bioRxiv. Microbiol. Pub Date : 2024-03-15 Sara M Klose, Alistair R Legione, Rhys N Bushell, Glenn F Browning, Paola K Vaz
Mycoplasma felis has been isolated from diseased cats and horses, but to date only a single fully assembled genome of this species, of an isolate from a horse, has been characterised. This study aimed to characterise and compare the completely assembled genomes of four clinical isolates of M. felis from three domestic cats, assembled with the aid of short and long read sequencing methods. The completed
-
Microbial nitrogen guilds in the oceans: from the bathypelagic to the ocean surface bioRxiv. Microbiol. Pub Date : 2024-03-15 Juan Rivas-Santisteban, Nuria Fernandez-Gonzalez, Rafael Laso-Perez, Javier Tamames, Carlos Pedros-Alio
Microbial nitrogen guilds play crucial roles in the oceanic nitrogen cycle, but their composition and importance across specific depths and conditions remain unclear. In this study, we examine the guilds participating in nitrogen transformations within the low and mid-latitude ocean ecosystems, from the surface down to 4000 m, using data obtained from 75 samples belonging to 11 stations in the Malaspina
-
Expanding the human gut microbiome atlas of Africa bioRxiv. Microbiol. Pub Date : 2024-03-14 Dylan G Maghini, Ovokeraye H Oduaran, Jakob Wirbel, Luicer A Ingasia Olubayo, Natalie Smyth, Theophilous Mathema, Carl W Belger, Godfred Agongo, Palwendé R Boua, Solomon SR Choma, F Xavier Gómez-Olivé, Isaac Kisiangani, Given R Mashaba, Lisa Micklesfield, Shukri F Mohamed, Engelbert A Nonterah, Shane Norris, Hermann Sorgho, Stephen Tollman, Floidy Wafawanaka, Furahini Tluway, Michèle Ramsay, Ami S
Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut
-
A Toolbox for Neisseria meningitidis: Gene Editing, Complementation and Labelling bioRxiv. Microbiol. Pub Date : 2024-03-14 Morgane Wuckelt, Audrey Laurent, Clemence Mouville, Julie Meyer, Anne Jamet, Herve Lecuyer, Xavier Nassif, Emmanuelle Bille, Vladimir Pelicic, Mathieu Coureuil
The efficient transformation of Neisseria meningitidis and Neisseria gonorrhoeae facilitates the rapid construction of bacterial mutants with insertion of antibiotic resistance cassettes. However, this strategy limits the construction of strains with multiple mutations. Recent advances in markerless strategies for Neisseria species have enabled the construction of mutants without antibiotic resistance
-
Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry bioRxiv. Microbiol. Pub Date : 2024-03-14 Angela Wang, Emily EF Fekete, Marybeth Creskey, Kai Cheng, Zhibin Ning, Annabelle Pfeifle, Xuguang Li, Daniel Figeys, Xu Zhang
Aim: This study aims to evaluate the impact of experimental workflow on fecal metaproteomic observations, including the recovery of small and antimicrobial proteins often overlooked in metaproteomic studies. The overarching goal is to provide guidance for optimized metaproteomic experimental design, considering the emerging significance of the gut microbiome in human health, disease, and therapeutic
-
The T4bSS of Legionella features a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectors bioRxiv. Microbiol. Pub Date : 2024-03-14 Samuel Wagner, Silke Malmsheimer, Iwan Grin, Erwin Bohn, Mirita Franz-Wachtel, Boris Macek, Tobias Sahr, Fabian Smollich, David Chetrit, Amit Meir, Craig Roy, Carmen Buchrieser
To promote intracellular survival and infection, Legionella spp. translocate hundreds of effector proteins into eukaryotic host cells using a type IV b protein secretion system (T4bSS). T4bSS are well known to translocate soluble as well as transmembrane domain-containing effector proteins (TMD-effectors) but the mechanisms of secretion are still poorly understood. Herein we investigated the secretion
-
A random mutagenesis screen enriched for missense mutations in bacterial effector proteins. bioRxiv. Microbiol. Pub Date : 2024-03-14 Malene L Urbanus, Thomas M Zheng, Anna N Khusnutdinova, Doreen Banh, Harley O'Connor Mount, Alind Gupta, Peter J Stogios, Alexei Savchenko, Ralph R Isberg, Alexander F Yakunin, Alexander W Ensminger
To remodel their hosts and escape immune defenses, many pathogens rely on large arsenals of proteins (effectors) that are delivered to the host cell using dedicated translocation machinery. Effectors hold significant insight into the biology of both the pathogens that encode for them and the host pathways that they manipulate. One of the most powerful systems biology tools for studying effectors is
-
The replication properties of a contemporary Zika virus from West Africa depends on NS1/NS4B proteins bioRxiv. Microbiol. Pub Date : 2024-03-14 Dana Machmouchi, Marie-Pierre Courageot, Chaker El-Kalamouni, Alain Kohl, Philippe Despres
Zika virus (ZIKV) have become a global health problem over the past decade due to the extension of the geographic distribution of ZIKV of Asian genotype. Epidemics of Asian ZIKV have been associated with developmental disorders in humans. ZIKV of African lineage would have an epidemic potential associated to fetal pathogenicity requiring a greater attention towards the most recently isolated viral
-
Escherichia coli grown in cost-effective conical tubes produces more plasmid DNA bioRxiv. Microbiol. Pub Date : 2024-03-14 Mayr Marquez, Qian Chen, Silvia Cachaco, Hongyan Sui, Tomozumi Imamichi
Before the COVID-19 pandemic, we grew plasmid-transformed Escherichia coli in Falcon round-bottom-polypropylene tubes (F-Round-PP) and isolated plasmid using a Miniprep kit. When obtaining sufficient quantities of F-Round-PP became problematic during the pandemic and the inflation, we grew them using any available tubes. Notably, we observed that plasmid yield from cells grown in a cost-effective Oxford
-
Versatile roles of protein flavinylation in bacterial extracyotosolic electron transfer bioRxiv. Microbiol. Pub Date : 2024-03-14 Shuo Huang, Raphaël Méheust, Blanca Barquera, Samuel H. Light
Bacteria perform diverse redox chemistries in the periplasm, cell wall, and extracellular space. Electron transfer for these extracytosolic activities is frequently mediated by proteins with covalently bound flavins, which are attached through post-translational flavinylation by the enzyme ApbE. Despite the significance of protein flavinylation to bacterial physiology, the basis and function of this
-
Identification of a new family of peptidoglycan transpeptidases reveals atypical crosslinking is essential for viability in Clostridioides difficile bioRxiv. Microbiol. Pub Date : 2024-03-14 Kevin W. Bollinger, Ute Muh, Karl L. Ocius, Alexis J. Apostolos, Marcos M. Pires, Richard F. Helm, David L Popham, David S. Weiss, Craig D. Ellermeier
Clostridioides difficile, the leading cause of antibiotic-associated diarrhea, relies primarily on 3-3 crosslinks created by L,D-transpeptidases (LDTs) to fortify its peptidoglycan (PG) cell wall. This is unusual, as in most bacteria the vast majority of PG crosslinks are 4-3 crosslinks, which are created by penicillin-binding proteins (PBPs). Here we report the unprecedented observation that 3-3 crosslinking
-
Functional assessment of cell entry and receptor use for merbecoviruses bioRxiv. Microbiol. Pub Date : 2024-03-14 Michael C Letko
The merbecovirus subgenus of coronaviruses includes Middle East Respiratory Syndrome Coronavirus (MERS-CoV), which is a zoonotic respiratory pathogen that transmits from dromedary camels to humans and causes severe respiratory disease. Viral discovery efforts have uncovered hundreds of merbecoviruses in different species across multiple continents, but few of these viruses have been isolated or studied
-
Assessing horizontal gene transfer in the rhizosphere of Brachypodium distachyon using fabricated ecosystems (EcoFABs) bioRxiv. Microbiol. Pub Date : 2024-03-14 Shweta Priya, Silvia Rossbach, Thomas Eng, Peter Andeer, Hsiao-Han Lin, Jenny Mortimer, Trent Northen, Aindrila Mukhopadhyay
Horizontal gene transfer (HGT) is a major process by which genes are transferred within microbes in the rhizosphere. However, examining HGT remains challenging due to the complexity of mimicking conditions within the rhizosphere. Fabricated ecosystems (EcoFABs) have been used to investigate several complex processes in plant associated environments. Here we show that EcoFABs are efficient tools to
-
Experimental evolution of a reduced bacterial chemotaxis network bioRxiv. Microbiol. Pub Date : 2024-03-14 Manika Kargeti, Irina Kalita, Sarah Hoch, Maryia Ratnikava, Wenhao Xu, Bin Ni, Ron Leonard Dy, Remy Colin, Victor Sourjik
Chemotaxis allows bacteria to follow chemical gradients by comparing their environment over time and adjusting their swimming behavior accordingly. The chemotaxis signaling pathway is highly conserved among all chemotactic bacteria. The system comprises two modules: one for environmental sensing and signal transduction toward the flagellar motor, and the other for adapting to the constant level of
-
Characterization of natural product inhibitors of quorum sensing in Pseudomonas aeruginosa reveals competitive inhibition of RhlR by ortho-vanillin bioRxiv. Microbiol. Pub Date : 2024-03-13 Kathryn E Woods, Sana Akhter, Blanca L Rodriguez, Kade A Townsend, Nathan C Smith, Alice N Wambua, Vaughn Craddock, Emma E Santa, Daniel E Manson, Rhea G Abisado-Duque, Berl R Oakley, Lynn E Hancock, Yinglong Miao, Helen E Blackwell, Josephine R Chandler
Quorum sensing (QS) is a cell-cell signaling system that enables bacteria to coordinate population density-dependent changes in behavior. This chemical communication pathway is mediated by diffusible N-acyl L-homoserine lactone signals and cytoplasmic signal-responsive LuxR-type receptors in Gram-negative bacteria. As many common pathogenic bacteria use QS to regulate virulence, there is significant
-
Decoding the complexity of delayed wound healing following Enterococcus faecalis infection bioRxiv. Microbiol. Pub Date : 2024-03-13 Cenk Celik, Stella Yue Ting Lee, Frederick Reinhart Tanoto, Mark Veleba, Kimberly A. Kline, Guillaume Thibault
Wound infections are highly prevalent, and can lead to delayed or failed healing, causing significant morbidity and adverse economic impacts. These infections occur in various contexts, including diabetic foot ulcers, burns, and surgical sites. Enterococcus faecalis is often found in persistent non-healing wounds, but its contribution to chronic wounds remains understudied. To address this, we employed
-
Root exudation and rhizosphere microbial recruitment are influenced by novel plant trait diversity in carrot genotypes bioRxiv. Microbiol. Pub Date : 2024-03-13 Hannah M. Anderson, Grace A. Cagle, Erica L.-W. Majumder, Erin Silva, Julie Dawson, Philipp Simon, Zachary B. Freedman
Root exudate composition can influence rhizosphere microbial recruitment and is tightly controlled by plant genetics. However, little research has profiled root exudate in vegetable crops or determined their role in rhizosphere microbial community and metabolite composition. It is also not well understood how root exudates and resulting rhizosphere dynamics shift across plant trait diversity and with
-
A vector system for single and tandem expression of cloned genes and multi-colour fluorescent tagging in Haloferax volcanii bioRxiv. Microbiol. Pub Date : 2024-03-13 Solenne Ithurbide, Roshali T. de Silva, Hannah J. Brown, Vinaya Shinde, Iain G. Duggin
Archaeal cell biology is an emerging field expected to identify fundamental cellular processes, help resolve the deep evolutionary history of cellular life, and contribute new components and functions in biotechnology and synthetic biology. To facilitate these, we have developed plasmid vectors that allow convenient cloning and production of proteins and fusion proteins with flexible, rigid, or semi-rigid
-
Genetic signatures in the highly virulent subtype B HIV-1 conferring immune escape to V1/V2 and V3 broadly neutralizing antibodies bioRxiv. Microbiol. Pub Date : 2024-03-13 Manukumar Marichannegowda, Alonso Heredia, Yin Wang, Hongshuo Song
HIV-1 is considered to become less susceptible to existing neutralizing antibodies over time. Our study on the virulent B (VB) HIV-1 identified genetic signatures responsible for immune escape from broadly neutralizing antibodies (bNAbs) targeting V1/V2 and V3 glycan epitopes. We found that the absence of N295 and N332 glycans in the high mannose patch, which are crucial for neutralization by V3 glycan
-
Searching the Pinus taeda foliar mycobiome for emerging pathogens among brown spot needle blight and needlecast outbreaks in the Southeast United States bioRxiv. Microbiol. Pub Date : 2024-03-13 Colton Daniel Meinecke, Afaq M. M. Niyas, Elizabeth McCarty, Tania Quesada, Jason A. Smith, Caterina Villari
Needle pathogens cause the discoloration, death, or premature abscission of conifer foliage, which reduce growth and vigor, and repeated defoliation may eventually result in tree mortality. Since 2016, forest managers in the southeast United States have reported an increasing scale, frequency, and severity of needle disease outbreaks on the regional principal timber species, loblolly pine (Pinus taeda
-
Divergent marine anaerobic ciliates harbor closely related Methanocorpusculum endosymbionts bioRxiv. Microbiol. Pub Date : 2024-03-13 Anna Schrecengost, Kateřina Poláková, Johana Rotterová, Ivan Čepička, Roxanne A Beinart
Ciliates are a diverse group of protists known for their ability to establish various partnerships and thrive in a wide variety of oxygen-depleted environments. Most anaerobic ciliates harbor methanogens, one of the few known archaea living intracellularly. These methanogens increase the metabolic efficiency of host fermentation via syntrophic use of host end-product in methanogenesis. Despite the
-
Applying 3D correlative structured illumination microscopy and X-ray tomography to characterise herpes simplex virus-1 morphogenesis bioRxiv. Microbiol. Pub Date : 2024-03-13 Kamal L Nahas, Vivienne Connor, Kaveesha J Wijesinghe, Henry G Barrow, Ian M Dobbie, Maria Harkiolaki, Stephen C Graham, Colin M Crump
Numerous viral genes are involved in assembly of herpes simplex virus-1 (HSV-1), but their relative importance and function remain poorly characterised. Transmission electron microscopy has been used to study viral protein function in cells infected with HSV-1 mutants; however, these studies were usually conducted without correlative light microscopy to identify specific viral components. In this study
-
The multifunction Coxiella effector Vice stimulates macropinocytosis and interferes with the ESCRT machinery bioRxiv. Microbiol. Pub Date : 2024-03-13 Arthur Bienvenu, Melanie Burette, Franck Cantet, Manon Gourdelier, Jitendriya M Swain, Chantal Cazevieille, Tatiana Clemente, Arif Sadi, Claire Dupont, Manon Le Fe, Nicolas Bonetto, Benoit Bordignon, Delphine MURIAUX, Stacey D Gilk, Matteo Bonazzi, Eric Martinez
Intracellular bacterial pathogens divert multiple cellular pathways to establish their niche and persist inside their host. Coxiella burnetii, the causative agent of Q fever, secretes bacterial effector proteins via its Type 4 secretion system to generate a Coxiella-containing vacuole (CCV). Manipulation of lipid and protein trafficking by these effectors is essential for bacterial replication and
-
The Structure of the Lujo Virus Spike Complex bioRxiv. Microbiol. Pub Date : 2024-03-13 Maayan Eilon-Ashkenazy, Hadas Cohen-Dvashi, Sarah Borni, Ron Shaked, Rivka Calinsky, Koby Levy, Ron Diskin
Lujo virus is a human pathogen that emerged as the etiology agent of a deadly viral disease in Africa. While it is a member of the Arenaviridae, it is a distinct virus that does not classify with the classical Old World or New World groups of viruses in this family. It further utilizes neuropilin-2 (NRP2) as an entry receptor, a property that is not shared by other arenaviruses. So far, structural
-
The Role of Ebola Virus VP24 Nuclear Trafficking Signals in Infectious Particle Production bioRxiv. Microbiol. Pub Date : 2024-03-13 Olivia A. Vogel, Elias Nafziger, Anurag Sharma, H. Amalia Pasolli, Robert A. Davey, Christopher F. Basler
Ebola virus (EBOV) protein VP24 carries out at least two critical functions. It promotes condensation of viral nucleocapsids, which is crucial for infectious virus production, and it suppresses interferon (IFN) signaling, which requires interaction with the NPI-1 subfamily of importin-a (IMPA) nuclear transport proteins. Interestingly, over-expressed IMPA leads to VP24 nuclear accumulation and a carboxy-terminus
-
De novo Genome Sequencing and Annotation of a Thermophilic Cyanobacterium using the Oxford Nanopore Technologies Sequencing Platform bioRxiv. Microbiol. Pub Date : 2024-03-13 Dirk Volker Woortman, Martha Kandawa-Schulz, Norbert Mehlmer, Thomas Brueck
In this project the MinION DNA sequencing platform was tested and introduced. It was proven that Next-Generation Sequencing (NGS) is not restricted to core facilities, but can be implemented in a standard laboratory setting. This makes the MinION suitable for decentralized strain screening, development and quality monitoring applications in the biotechnology industry. Over the course of the MinION
-
Spatial integration of sensory input and motor output in Pseudomonas aeruginosa chemotaxis through colocalized distribution bioRxiv. Microbiol. Pub Date : 2024-03-13 Zhengyu Wu, Maojin Tian, Sanyuan Fu, Min Chen, Rongjing Zhang, Junhua Yuan
The opportunistic pathogen Pseudomonas aeruginosa serves as a model organism for studying multiple signal transduction pathways. The chemoreceptor cluster, a core component of the chemotaxis pathway, is assembled from hundreds of proteins. The unipolar distribution of receptor clusters has long been recognized, yet the precise mechanism governing their assembly remains elusive. Here, we directly observed
-
Detection of oat crown rust disease in Taiwan (2019-2021) bioRxiv. Microbiol. Pub Date : 2024-03-13 Chung-Ying Ho, Eva Henningsen, Ssu-Tung Chen, Hiran A Ariyawansa, Eric C Nazareno, Jana Sperschneider, Peter Dodds, Jakob M Riddle, Shahryar F Kianian, Melania Figueroa, Yung-Fen Huang
Oat is a minor forage crop grown in Taiwan. Only a few historical records of oat rust disease have been reported in the country, therefore the pathogen population remains poorly characterized. A rust-like disease outbreak was detected at the Experimental Farm of National Taiwan University in 2019, which caused significant damage to the field experiments. To determine the identity of the pathogen responsible
-
Changes in the senescence profile and immune checkpoints in HIV-infected individuals after COVID-19 bioRxiv. Microbiol. Pub Date : 2024-03-13 Celia Crespo-Bermejo, Oscar Brochado-Kith, Sergio Grande-Garcia, Violeta Lara-Aguilar, Manuel Llamas-Adan, Sonia Arca-Lafuente, Luz Martin-Carbonero, Ignacio de los Santos, M Angeles Jimenez Sousa, Salvador Resino, Juan Berenguer, Ricardo Madrid, Amanda Fernandez-Rodriguez, Veronica Briz
Background: Both SARS-CoV-2 and HIV infection exhibit alterations in the senescence profile and immune checkpoint (IC) molecules. However, the midterm impact of SARS-CoV-2 on these profiles in people with HIV (PWH) remains unclear. This study aimed to evaluate differences in plasma biomarker levels related to ICs, the senescence-associated secretory phenotype (SASP), and pro- and anti-inflammatory