Pub Date : 2024-09-12DOI: 10.1101/2024.09.12.612726
Joseph Ulbrich, Nathaniel E. Jobe, Daniel Seth Jones, Thomas L. Kieft
Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.
{"title":"Cave pools in Carlsbad Caverns National Park contain diverse bacteriophage communities and novel viral sequences","authors":"Joseph Ulbrich, Nathaniel E. Jobe, Daniel Seth Jones, Thomas L. Kieft","doi":"10.1101/2024.09.12.612726","DOIUrl":"https://doi.org/10.1101/2024.09.12.612726","url":null,"abstract":"Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.09.12.612678
Deepak Kumar Choudhary, Himani Singla, Dana Vassover, Noam Golan, Leah Reshef, Vadim Dubunsky, Uri Gophna
Many cyclic-oligonucleotide-based antiphage signalling systems (CBASS) defend against viral infections using a TIR-SAVED domain protein that depletes cellular NAD+ levels, eventually leading to cell dormancy or death. This abortive infection strategy is beneficial in stopping fast lytic infections, as cells die before spreading the virus to neighboring cells. However, many archaea are infected by chronic "temperate" viruses that coexist with their hosts for extended periods. In such situations, abortive infection could be detrimental, as the cost of immunity may outweigh that of infection. In this study, we examine an archaeal Type II-C CBASS system from Haloferax strain Atlit 48N that was heterologously expressed in the model organism Haloferax volcanii DS2. We demonstrate that this system protects against a chronically infecting virus, HFPV-1, and enables clearing of the virus after several passages without killing the host. Moreover, cells that have cleared the virus become substantially more resistant to future HFPV-1 infections, without acquiring CRISPR spacers from that virus. Cell death during viral infection only occurs after extensive incubation with HFPV-1. These findings suggest that CBASS could be beneficial even for archaea exposed to chronic infecting viruses, potentially explaining why such systems are relatively common in archaea.
{"title":"An archaeal CBASS system eliminates viruses without killing the host cells","authors":"Deepak Kumar Choudhary, Himani Singla, Dana Vassover, Noam Golan, Leah Reshef, Vadim Dubunsky, Uri Gophna","doi":"10.1101/2024.09.12.612678","DOIUrl":"https://doi.org/10.1101/2024.09.12.612678","url":null,"abstract":"Many cyclic-oligonucleotide-based antiphage signalling systems (CBASS) defend against viral infections using a TIR-SAVED domain protein that depletes cellular NAD+ levels, eventually leading to cell dormancy or death. This abortive infection strategy is beneficial in stopping fast lytic infections, as cells die before spreading the virus to neighboring cells. However, many archaea are infected by chronic \"temperate\" viruses that coexist with their hosts for extended periods. In such situations, abortive infection could be detrimental, as the cost of immunity may outweigh that of infection. In this study, we examine an archaeal Type II-C CBASS system from Haloferax strain Atlit 48N that was heterologously expressed in the model organism Haloferax volcanii DS2. We demonstrate that this system protects against a chronically infecting virus, HFPV-1, and enables clearing of the virus after several passages without killing the host. Moreover, cells that have cleared the virus become substantially more resistant to future HFPV-1 infections, without acquiring CRISPR spacers from that virus. Cell death during viral infection only occurs after extensive incubation with HFPV-1. These findings suggest that CBASS could be beneficial even for archaea exposed to chronic infecting viruses, potentially explaining why such systems are relatively common in archaea.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.09.11.612458
Roberto Jhonatan Olea-Ozuna, Melanie J Campbell, Samantha Y Quintanilla, Sinjini Nandy, Jennifer S Brodbelt, Joseph M Boll
The Gram-negative outer membrane protects bacterial cells from environmental toxins such as antibiotics. The outer membrane lipid bilayer is asymmetric; while glycerophospholipids compose the periplasmic facing leaflet, the surface layer is enriched with phosphate-containing lipopolysaccharides. The anionic phosphates that decorate the cell surface promote electrostatic interactions with cationic antimicrobial peptides such as colistin, allowing them to penetrate the bilayer, form pores, and lyse the cell. Colistin is prescribed as a last-line therapy to treat multidrug-resistant Gram-negative infections. Acinetobacter baumannii is an ESKAPE pathogen that rapidly develops resistance to antibiotics and persists for extended periods in the host or on abiotic surfaces. Survival in environmental stress such as phosphate scarcity, represents a clinically significant challenge for nosocomial pathogens. In the face of phosphate starvation, certain bacteria encode adaptive strategies, including the substitution of glycerophospholipids with phosphorus-free lipids. In bacteria, phosphatidylethanolamine, phosphatidylglycerol, and cardiolipin are conserved glycerophospholipids that form lipid bilayers. Here, we demonstrate that in response to phosphate limitation, conserved regulatory mechanisms induce aminolipid production in A. baumannii. Specifically, phosphate limitation induces formation of three lipids, including amine-containing ornithine and lysine aminolipids. Mutations that inactivate aminolipid biosynthesis exhibit fitness defects relative to wild type in colistin growth and killing assays. Furthermore, we show that other Gram-negative ESKAPE pathogens accumulate aminolipids under phosphate limiting growth conditions, suggesting aminolipid biosynthesis may represent a broad strategy to overcome cationic antimicrobial peptide-mediated killing.
{"title":"Alternative lipid synthesis in response to phosphate limitation promotes antibiotic tolerance in Gram-negative ESKAPE pathogens","authors":"Roberto Jhonatan Olea-Ozuna, Melanie J Campbell, Samantha Y Quintanilla, Sinjini Nandy, Jennifer S Brodbelt, Joseph M Boll","doi":"10.1101/2024.09.11.612458","DOIUrl":"https://doi.org/10.1101/2024.09.11.612458","url":null,"abstract":"The Gram-negative outer membrane protects bacterial cells from environmental toxins such as antibiotics. The outer membrane lipid bilayer is asymmetric; while glycerophospholipids compose the periplasmic facing leaflet, the surface layer is enriched with phosphate-containing lipopolysaccharides. The anionic phosphates that decorate the cell surface promote electrostatic interactions with cationic antimicrobial peptides such as colistin, allowing them to penetrate the bilayer, form pores, and lyse the cell. Colistin is prescribed as a last-line therapy to treat multidrug-resistant Gram-negative infections. <em>Acinetobacter baumannii</em> is an ESKAPE pathogen that rapidly develops resistance to antibiotics and persists for extended periods in the host or on abiotic surfaces. Survival in environmental stress such as phosphate scarcity, represents a clinically significant challenge for nosocomial pathogens. In the face of phosphate starvation, certain bacteria encode adaptive strategies, including the substitution of glycerophospholipids with phosphorus-free lipids. In bacteria, phosphatidylethanolamine, phosphatidylglycerol, and cardiolipin are conserved glycerophospholipids that form lipid bilayers. Here, we demonstrate that in response to phosphate limitation, conserved regulatory mechanisms induce aminolipid production in <em>A. baumannii</em>. Specifically, phosphate limitation induces formation of three lipids, including amine-containing ornithine and lysine aminolipids. Mutations that inactivate aminolipid biosynthesis exhibit fitness defects relative to wild type in colistin growth and killing assays. Furthermore, we show that other Gram-negative ESKAPE pathogens accumulate aminolipids under phosphate limiting growth conditions, suggesting aminolipid biosynthesis may represent a broad strategy to overcome cationic antimicrobial peptide-mediated killing.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.09.12.612603
George F Aranjuez, Om Patel, Dev Patel, Travis J Jewett
Chlamydia trachomatis is an obligate, intracellular Gram-negative bacteria and the leading bacterial STI in the United States. Chlamydia’s developmental cycle involves host cell entry, replication within a parasitophorous vacuole called an inclusion, and induction of host cell lysis to release new infectious particles. During development, Chlamydia manipulates the host cell biology using various secreted bacterial effectors. The early effector Tarp is important for Chlamydia entry via its well-characterized C-terminal region which can polymerize and bundle F-actin. In contrast, not much is known about the function of Tarp’s N-terminus (N-Tarp), though this N-terminal region is present in many Chlamydia species. To address this, we use Drosophila melanogaster as an in vivo cell biology platform to study N-Tarp-host interactions. Drosophila development is well-characterized such that developmental phenotypes can be traced back to the perturbed molecular pathway. Transgenic expression of N-Tarp in Drosophila tissues results in phenotypes consistent with altered host Hippo signaling. The Salvador-Warts-Hippo pathway is a conserved signaling cascade that regulates host cell proliferation and survival during normal animal development. We studied N-Tarp function in larval imaginal wing discs, which are sensitive to perturbations in Hippo signaling. N-Tarp causes wing disc overgrowth and a concomitant increase in adult wing size, phenocopying overexpression of the Hippo co-activator Yorkie. N-Tarp also causes upregulation of Hippo target genes. Last, N-Tarp-induced phenotypes can be rescued by reducing the levels of Yorkie, or the Hippo target genes CycE and Diap1. Thus, we provide the first evidence that the N-terminal region of the Chlamydia effector Tarp is sufficient to alter host Hippo signaling and acts upstream of the co-activator Yorkie. Chlamydia alters host cell apoptosis during infection, though the exact mechanism remains unknown. Our findings implicate the N-terminal region of Tarp as a way to manipulate the host Hippo signaling pathway, which directly influences cell survival.
沙眼衣原体是一种必须的细胞内革兰氏阴性细菌，也是美国主要的细菌性 STI。衣原体的发育周期包括进入宿主细胞、在称为包涵体的寄生泡内复制、诱导宿主细胞裂解以释放新的感染性颗粒。在发育过程中，衣原体利用各种分泌的细菌效应器操纵宿主细胞的生物学特性。早期效应物 Tarp 对衣原体的进入非常重要，因为它的 C 端区域具有良好的特性，可以聚合和捆绑 F-肌动蛋白。相比之下，人们对 Tarp 的 N-末端（N-Tarp）的功能知之甚少，尽管许多衣原体种类都存在 N-末端区域。为了解决这个问题，我们利用黑腹果蝇作为体内细胞生物学平台来研究 N-Tarp 与宿主的相互作用。果蝇的发育特征良好，因此发育表型可以追溯到受干扰的分子途径。在果蝇组织中转基因表达 N-Tarp 会导致与宿主 Hippo 信号改变一致的表型。萨尔瓦多-瓦兹-希波信号通路是一种保守的信号级联，在正常动物发育过程中调节宿主细胞的增殖和存活。我们研究了N-Tarp在幼虫意象翼盘中的功能，意象翼盘对Hippo信号的扰动很敏感。N-Tarp会导致翼盘过度生长，同时增加成体翅膀的大小，表型类似于Hippo共激活剂Yorkie的过度表达。N-Tarp 还会导致 Hippo 靶基因上调。最后，N-Tarp诱导的表型可以通过降低Yorkie或Hippo靶基因CycE和Diap1的水平来挽救。因此，我们首次证明衣原体效应物 Tarp 的 N 端区域足以改变宿主的 Hippo 信号传导，并作用于共激活因子 Yorkie 的上游。衣原体会在感染过程中改变宿主细胞的凋亡，但其确切机制仍不清楚。我们的研究结果表明，Tarp 的 N 端区域是操纵宿主 Hippo 信号通路的一种方式，而 Hippo 信号通路会直接影响细胞的存活。
{"title":"The N-terminus of the Chlamydia trachomatis effector Tarp engages the host Hippo pathway","authors":"George F Aranjuez, Om Patel, Dev Patel, Travis J Jewett","doi":"10.1101/2024.09.12.612603","DOIUrl":"https://doi.org/10.1101/2024.09.12.612603","url":null,"abstract":"Chlamydia trachomatis is an obligate, intracellular Gram-negative bacteria and the leading bacterial STI in the United States. Chlamydia’s developmental cycle involves host cell entry, replication within a parasitophorous vacuole called an inclusion, and induction of host cell lysis to release new infectious particles. During development, Chlamydia manipulates the host cell biology using various secreted bacterial effectors. The early effector Tarp is important for Chlamydia entry via its well-characterized C-terminal region which can polymerize and bundle F-actin. In contrast, not much is known about the function of Tarp’s N-terminus (N-Tarp), though this N-terminal region is present in many Chlamydia species. To address this, we use Drosophila melanogaster as an in vivo cell biology platform to study N-Tarp-host interactions. Drosophila development is well-characterized such that developmental phenotypes can be traced back to the perturbed molecular pathway. Transgenic expression of N-Tarp in Drosophila tissues results in phenotypes consistent with altered host Hippo signaling. The Salvador-Warts-Hippo pathway is a conserved signaling cascade that regulates host cell proliferation and survival during normal animal development. We studied N-Tarp function in larval imaginal wing discs, which are sensitive to perturbations in Hippo signaling. N-Tarp causes wing disc overgrowth and a concomitant increase in adult wing size, phenocopying overexpression of the Hippo co-activator Yorkie. N-Tarp also causes upregulation of Hippo target genes. Last, N-Tarp-induced phenotypes can be rescued by reducing the levels of Yorkie, or the Hippo target genes CycE and Diap1. Thus, we provide the first evidence that the N-terminal region of the Chlamydia effector Tarp is sufficient to alter host Hippo signaling and acts upstream of the co-activator Yorkie. Chlamydia alters host cell apoptosis during infection, though the exact mechanism remains unknown. Our findings implicate the N-terminal region of Tarp as a way to manipulate the host Hippo signaling pathway, which directly influences cell survival.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.09.12.612594
Hassan Hakimi, Pabasara Weerarathne, Meriam N. Saleh, Raquel R. Rech, Richard R. Ngandolo Bongo Nare, Philip R. Ouakou Tchindebet, Sidouin K. Metinou, Lucienne Tritten, Guilherme Gomes Verocai
Guinea worm (GW, Dracunculus medinensis) is a nematode that causes a painful and debilitating neglected tropical disease in humans. The GW Eradication Program has decreased human infections by >99% over the last 40 years. However, GW emergence in animal hosts, particularly dogs, has hampered eradication efforts. Currently, there is no method for diagnosing GW infection in animals during the prepatent period, before the adult female worms emerge. Previous works have identified two GW proteins, TRX and DUF148, as immunoreactive antigens with GW-positive human and dog sera. This study developed and validated indirect enzyme-linked immunosorbent assays (ELISA) using each antigen alone or in a combination of both antigens. Using serum samples from experimentally exposed dogs, TRX and DUF148 showed reactivity at 9- and 11-weeks post-exposure, respectively. In an experimentally infected ferret, TRX and DUF148 showed reactivity at 13- and 15-weeks post-exposure, respectively. These antigens were further validated using sera of dogs from endemic villages in Chad (n=47) and shelter dogs from the non-endemic United States (n=492). DUF148 showed better reactivity and sensitivity of 76.6.% in detecting GW infection in prepatent sera compared to TRX. However, DUF148 cross-reacted with one serum sample from Brugia pahangi experimental infection and several shelter dog sera. The anti-DUF148 titer was significantly higher in the shelter dogs positive for gastrointestinal nematodes than in negative dogs. To mitigate this cross-reaction, we produced 3 peptides of DUF148. Peptide 3 from the C-terminal was more reactive with prepatent sera and had a sensitivity of 83%; however, the specificity was not superior to DUF148 whole antigen. The antibody response to DUF148 in Chad dogs with the history of GW emergence waned overtime but was detectable until two years post-GW-emergence. Our findings could facilitate the development of diagnostic methods for early detection of GW infection in dogs in endemic countries.
{"title":"Assessing the performance of TRX and DUF148 antigens for detection of prepatent Guinea worm (Dracunculus medinensis) infection in dogs","authors":"Hassan Hakimi, Pabasara Weerarathne, Meriam N. Saleh, Raquel R. Rech, Richard R. Ngandolo Bongo Nare, Philip R. Ouakou Tchindebet, Sidouin K. Metinou, Lucienne Tritten, Guilherme Gomes Verocai","doi":"10.1101/2024.09.12.612594","DOIUrl":"https://doi.org/10.1101/2024.09.12.612594","url":null,"abstract":"Guinea worm (GW, Dracunculus medinensis) is a nematode that causes a painful and debilitating neglected tropical disease in humans. The GW Eradication Program has decreased human infections by >99% over the last 40 years. However, GW emergence in animal hosts, particularly dogs, has hampered eradication efforts. Currently, there is no method for diagnosing GW infection in animals during the prepatent period, before the adult female worms emerge. Previous works have identified two GW proteins, TRX and DUF148, as immunoreactive antigens with GW-positive human and dog sera. This study developed and validated indirect enzyme-linked immunosorbent assays (ELISA) using each antigen alone or in a combination of both antigens. Using serum samples from experimentally exposed dogs, TRX and DUF148 showed reactivity at 9- and 11-weeks post-exposure, respectively. In an experimentally infected ferret, TRX and DUF148 showed reactivity at 13- and 15-weeks post-exposure, respectively. These antigens were further validated using sera of dogs from endemic villages in Chad (n=47) and shelter dogs from the non-endemic United States (n=492). DUF148 showed better reactivity and sensitivity of 76.6.% in detecting GW infection in prepatent sera compared to TRX. However, DUF148 cross-reacted with one serum sample from Brugia pahangi experimental infection and several shelter dog sera. The anti-DUF148 titer was significantly higher in the shelter dogs positive for gastrointestinal nematodes than in negative dogs. To mitigate this cross-reaction, we produced 3 peptides of DUF148. Peptide 3 from the C-terminal was more reactive with prepatent sera and had a sensitivity of 83%; however, the specificity was not superior to DUF148 whole antigen. The antibody response to DUF148 in Chad dogs with the history of GW emergence waned overtime but was detectable until two years post-GW-emergence. Our findings could facilitate the development of diagnostic methods for early detection of GW infection in dogs in endemic countries.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.09.12.612730
Jamie J.M. Lustermans, Naja Basu, Kartik Aiyer
Microbacteriaceae are a class of metabolically versatile gram-positive bacteria found in diverse environments. In sediments populated with filamentous cable bacteria, electric interspecies interactions between microbes and cable bacteria have been suggested. A novel, gram-positive bacterium, Microbacterium deferre strain A1-JK was isolated from the vicinity of a cable bacterium filament, capable of extracellular electron transfer (EET) to Fe(III) oxides and electrodes. Electrochemical experiments with pure cultures of M.deferre A1-JK in three-electrode cells revealed the presence of soluble mediators diffusing through the cell wall, identified through HPLC analysis as flavins. Genomic analyses further uncovered the complete riboflavin synthesis pathway, with heightened flavin production observed under oxygen-limited conditions to facilitate EET. M. deferre A1-JK encodes the periplasmic cytochrome FccA, responsible for transferring electrons on flavin carriers. M. deferre A1-JK exhibited a fast switch from aerobic metabolism to EET-based metabolism, aside from demonstrating weak electroactivity in alkaline (pH 8-10) and saline (4% NaCl) conditions. These results underscore its adaptability to use EET as an efficient survival strategy to deal with rapidly fluctuating sediment environments. These results hold promise for elucidating metabolic dynamics at oxic-anoxic interfaces along with further understanding of biogeochemical cycling in sediments.
{"title":"A flavin-based extracellular electron transfer strategy in a novel gram-positive microbe Microbacterium deferre sp. nov. strain A1-JK, isolated from cable bacteria enrichments","authors":"Jamie J.M. Lustermans, Naja Basu, Kartik Aiyer","doi":"10.1101/2024.09.12.612730","DOIUrl":"https://doi.org/10.1101/2024.09.12.612730","url":null,"abstract":"Microbacteriaceae are a class of metabolically versatile gram-positive bacteria found in diverse environments. In sediments populated with filamentous cable bacteria, electric interspecies interactions between microbes and cable bacteria have been suggested. A novel, gram-positive bacterium, Microbacterium deferre strain A1-JK was isolated from the vicinity of a cable bacterium filament, capable of extracellular electron transfer (EET) to Fe(III) oxides and electrodes. Electrochemical experiments with pure cultures of M.deferre A1-JK in three-electrode cells revealed the presence of soluble mediators diffusing through the cell wall, identified through HPLC analysis as flavins. Genomic analyses further uncovered the complete riboflavin synthesis pathway, with heightened flavin production observed under oxygen-limited conditions to facilitate EET. M. deferre A1-JK encodes the periplasmic cytochrome FccA, responsible for transferring electrons on flavin carriers. M. deferre A1-JK exhibited a fast switch from aerobic metabolism to EET-based metabolism, aside from demonstrating weak electroactivity in alkaline (pH 8-10) and saline (4% NaCl) conditions. These results underscore its adaptability to use EET as an efficient survival strategy to deal with rapidly fluctuating sediment environments. These results hold promise for elucidating metabolic dynamics at oxic-anoxic interfaces along with further understanding of biogeochemical cycling in sediments.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.09.12.612600
Raheel Asghar, Nan Wu, Noman Ali, Yulei Wang, Mahinur Akkaya
Understanding the biological functions of Puccinia striiformis f. sp. tritici (Pst) effectors is fundamental for uncovering the mechanisms of pathogenicity and variability, thereby paving the way for developing durable and effective control strategies for stripe rust. However, due to the lack of an efficient genetic transformation system in Pst, progress in effector function studies has been slow. Here, we modeled the structures of 15,201 effectors from twelve Pst races or isolates, a Puccinia striiformis isolate, and one Puccinia striiformis f. sp. hordei isolate using AlphaFold2. Of these, 8,102 folds were successfully predicted, and we performed sequence- and structure-based annotations of these effectors. These effectors were classified into 410 structure clusters and 1,005 sequence clusters. Sequence lengths varied widely, with a concentration between 101-250 amino acids, and motif analysis revealed the presence of known effector motifs such as [Y/F/W]xC and RxLR. Subcellular localization predictions indicated a predominant cytoplasmic localization, with notable chloroplast and nuclear presence. Clear annotations based on sequence and structure included superoxide dismutase and trehalose-6-phosphate phosphatase. A common feature observed was the formation of similar structures from different sequences. In our study, one of the comparative structural analyses revealed a new structure family with a core structure of four helices, including Pst27791, PstGSRE4, and PstSIE1, which target key wheat immune pathway proteins, impacting the host immune function. Further comparative structural analysis showed similarities between Pst effectors and effectors from other pathogens such as AvrSr35, AvrSr50, Zt-KP4-1, and MoHrip2, highlighting convergent evolutionary strategies. This comprehensive analysis provides novel insights into Pst effectors' structural and functional characterization, advancing our understanding of Pst pathogenicity and evolution.
{"title":"Computational studies reveal structural characterization and novel families of Puccinia striiformis f. sp. tritici effectors","authors":"Raheel Asghar, Nan Wu, Noman Ali, Yulei Wang, Mahinur Akkaya","doi":"10.1101/2024.09.12.612600","DOIUrl":"https://doi.org/10.1101/2024.09.12.612600","url":null,"abstract":"Understanding the biological functions of Puccinia striiformis f. sp. tritici (Pst) effectors is fundamental for uncovering the mechanisms of pathogenicity and variability, thereby paving the way for developing durable and effective control strategies for stripe rust. However, due to the lack of an efficient genetic transformation system in Pst, progress in effector function studies has been slow. Here, we modeled the structures of 15,201 effectors from twelve Pst races or isolates, a Puccinia striiformis isolate, and one Puccinia striiformis f. sp. hordei isolate using AlphaFold2. Of these, 8,102 folds were successfully predicted, and we performed sequence- and structure-based annotations of these effectors. These effectors were classified into 410 structure clusters and 1,005 sequence clusters. Sequence lengths varied widely, with a concentration between 101-250 amino acids, and motif analysis revealed the presence of known effector motifs such as [Y/F/W]xC and RxLR. Subcellular localization predictions indicated a predominant cytoplasmic localization, with notable chloroplast and nuclear presence. Clear annotations based on sequence and structure included superoxide dismutase and trehalose-6-phosphate phosphatase. A common feature observed was the formation of similar structures from different sequences. In our study, one of the comparative structural analyses revealed a new structure family with a core structure of four helices, including Pst27791, PstGSRE4, and PstSIE1, which target key wheat immune pathway proteins, impacting the host immune function. Further comparative structural analysis showed similarities between Pst effectors and effectors from other pathogens such as AvrSr35, AvrSr50, Zt-KP4-1, and MoHrip2, highlighting convergent evolutionary strategies. This comprehensive analysis provides novel insights into Pst effectors' structural and functional characterization, advancing our understanding of Pst pathogenicity and evolution.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
To address chlorophenol wastewater pollution, immobilized mixed white rot fungi (WRF) strain microsphere was designed as a solid degradation agent, using lignin peroxidase (LiP), manganese peroxidase (MnP), and laccase (Lac) to degradating the wastewater. Considering the diverse physical and chemical properties of the fungal sphere, the immobilization agent formula is optimized and comprehensive environmental factor design response surface analysis are implemented to determine the delivery conditions. Consequently, the 2,4-DCP treatment rate and extracellular enzyme activity for a 1:1 encapsulation of T. versicolor and P. sajor-caju significantly outperform those of individual strains. Using polyvinyl alcohol (PVA), sodium alginate (SA), and biochar as carriers, with sodium dihydrogen phosphate solution as crosslinker and SiO2/zeolite as additives, immobilizing mixed bacteria yielded a high-quality solid agent. This achieved a 99.33% 2,4-DCP degradation rate over 96 hours, with optimal dosage, pH, and initial 2,4-DCP concentration at 11.5 g/L, 5.5, and 40 mg/L. The degradation of 2,4-DCP by WRF selectively removes adjacent chlorine atoms to produce 4-CP, enhancing the dechlorination efficiency.
{"title":"Enzymatic Degrading Chlorophenol Wastewater by Mixed Strains of Immobilized White Rot Fungi","authors":"Hongyuan Liu, Xueyi Lou, Yeyao Shao, Zhichao Wang, Jiamin Xiao, Kai Cen, Dingyin Chen, Qiman Xia, Wenlong Xu, Fang Fang, Yasin Orooji, Peng Liu","doi":"10.1101/2024.09.09.611973","DOIUrl":"https://doi.org/10.1101/2024.09.09.611973","url":null,"abstract":"To address chlorophenol wastewater pollution, immobilized mixed white rot fungi (WRF) strain microsphere was designed as a solid degradation agent, using lignin peroxidase (LiP), manganese peroxidase (MnP), and laccase (Lac) to degradating the wastewater. Considering the diverse physical and chemical properties of the fungal sphere, the immobilization agent formula is optimized and comprehensive environmental factor design response surface analysis are implemented to determine the delivery conditions. Consequently, the 2,4-DCP treatment rate and extracellular enzyme activity for a 1:1 encapsulation of T. versicolor and P. sajor-caju significantly outperform those of individual strains. Using polyvinyl alcohol (PVA), sodium alginate (SA), and biochar as carriers, with sodium dihydrogen phosphate solution as crosslinker and SiO2/zeolite as additives, immobilizing mixed bacteria yielded a high-quality solid agent. This achieved a 99.33% 2,4-DCP degradation rate over 96 hours, with optimal dosage, pH, and initial 2,4-DCP concentration at 11.5 g/L, 5.5, and 40 mg/L. The degradation of 2,4-DCP by WRF selectively removes adjacent chlorine atoms to produce 4-CP, enhancing the dechlorination efficiency.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-11DOI: 10.1101/2024.09.11.612454
Owen Leddy, Yuko Yuki, Mary Carrington, Bryan D Bryson, Forest M White
Vaccine-elicited T cell responses can contribute to immune protection against emerging infectious disease risks such as antimicrobials-resistant (AMR) microbial pathogens and viruses with pandemic potential, but rapidly identifying appropriate targets for T cell priming vaccines remains challenging. Mass spectrometry (MS) analysis of peptides presented on major histocompatibility complexes (MHCs) can identify potential targets for protective T cell responses in a proteome-wide manner. However, pathogen-derived peptides are outnumbered by self peptides in the MHC repertoire and may be missed in untargeted MS analyses. Here we present a novel approach, termed PathMHC, that uses computational analysis of untargeted MS data followed by targeted MS to discover novel pathogen-derived MHC peptides more efficiently than untargeted methods alone. We applied this workflow to identify MHC peptides derived from multiple microbes, including potential vaccine targets presented on MHC-I by human dendritic cells infected with Mycobacterium tuberculosis. PathMHC will facilitate antigen discovery campaigns for vaccine development.
疫苗诱导的 T 细胞反应有助于提供免疫保护，抵御新出现的传染病风险，如抗菌素耐药 (AMR) 微生物病原体和具有大流行潜力的病毒，但快速确定 T 细胞诱导疫苗的适当靶点仍具有挑战性。对主要组织相容性复合体（MHC）上呈现的肽进行质谱分析，可以在整个蛋白质组范围内确定保护性 T 细胞反应的潜在靶点。然而，病原体衍生肽的数量超过了主要组织相容性复合物中自身肽的数量，可能会在非靶向 MS 分析中被漏掉。在这里，我们提出了一种称为 PathMHC 的新方法，它利用对非靶向 MS 数据的计算分析，然后再进行靶向 MS 分析，从而比单独使用非靶向方法更有效地发现新型病原体衍生的 MHC 肽。我们将这一工作流程用于鉴定来自多种微生物的 MHC 肽，包括感染结核分枝杆菌的人类树突状细胞在 MHC-I 上呈现的潜在疫苗靶标。PathMHC 将促进疫苗开发的抗原发现活动。
{"title":"PathMHC: a workflow to selectively target pathogen-derived MHC peptides in discovery immunopeptidomics experiments for vaccine target identification","authors":"Owen Leddy, Yuko Yuki, Mary Carrington, Bryan D Bryson, Forest M White","doi":"10.1101/2024.09.11.612454","DOIUrl":"https://doi.org/10.1101/2024.09.11.612454","url":null,"abstract":"Vaccine-elicited T cell responses can contribute to immune protection against emerging infectious disease risks such as antimicrobials-resistant (AMR) microbial pathogens and viruses with pandemic potential, but rapidly identifying appropriate targets for T cell priming vaccines remains challenging. Mass spectrometry (MS) analysis of peptides presented on major histocompatibility complexes (MHCs) can identify potential targets for protective T cell responses in a proteome-wide manner. However, pathogen-derived peptides are outnumbered by self peptides in the MHC repertoire and may be missed in untargeted MS analyses. Here we present a novel approach, termed PathMHC, that uses computational analysis of untargeted MS data followed by targeted MS to discover novel pathogen-derived MHC peptides more efficiently than untargeted methods alone. We applied this workflow to identify MHC peptides derived from multiple microbes, including potential vaccine targets presented on MHC-I by human dendritic cells infected with Mycobacterium tuberculosis. PathMHC will facilitate antigen discovery campaigns for vaccine development.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-11DOI: 10.1101/2024.09.11.612360
Marit A. K. Hetland, Mia A. Winkler, Hakon Kaspersen, Fredrik Hakonsholm, Ragna-Johanne Bakksjo, Eva Bernhoff, Jose F. Delgado-Blas, Sylvain Brisse, Annapaula Correia, Aasmund Fostervold, Margaret M. C. Lam, Bjorn-Tore Lunestad, Nachiket P. Marathe, Niclas Raffelsberger, Orjan Samuelsen, Marianne Sunde, Arnfinn Sundsfjord, Anne Margrete Urdahl, Ryan R. Wick, Iren H. Lohr, Kathryn E. Holt
Members of the Klebsiella pneumoniae species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC are common in non-human niches, but the clinical relevance of these populations is disputed. Utilising 3,255 whole-genome sequenced isolates from human, animal and marine sources collected during 2001-2020 in Norway, we showed the KpSC populations in different niches were distinct but overlapping. Notably, human infection isolates showed greatest connectivity with each other, followed by isolates from human carriage, pigs, and bivalves. Nearly 5% of human infection isolates had close relatives (≤22 substitutions) amongst animal and marine isolates, despite temporally and geographically distant sampling of these sources. Infection prevention measures are essential to limit transmission within human clinical settings and reduce disease burden. However, as colonisation often precedes infection, preventing transmission that leads to colonisation, e.g. transmission between animals and humans in the community, and in the food chain, could also be beneficial.
{"title":"A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs","authors":"Marit A. K. Hetland, Mia A. Winkler, Hakon Kaspersen, Fredrik Hakonsholm, Ragna-Johanne Bakksjo, Eva Bernhoff, Jose F. Delgado-Blas, Sylvain Brisse, Annapaula Correia, Aasmund Fostervold, Margaret M. C. Lam, Bjorn-Tore Lunestad, Nachiket P. Marathe, Niclas Raffelsberger, Orjan Samuelsen, Marianne Sunde, Arnfinn Sundsfjord, Anne Margrete Urdahl, Ryan R. Wick, Iren H. Lohr, Kathryn E. Holt","doi":"10.1101/2024.09.11.612360","DOIUrl":"https://doi.org/10.1101/2024.09.11.612360","url":null,"abstract":"Members of the <em>Klebsiella pneumoniae</em> species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC are common in non-human niches, but the clinical relevance of these populations is disputed. Utilising 3,255 whole-genome sequenced isolates from human, animal and marine sources collected during 2001-2020 in Norway, we showed the KpSC populations in different niches were distinct but overlapping. Notably, human infection isolates showed greatest connectivity with each other, followed by isolates from human carriage, pigs, and bivalves. Nearly 5% of human infection isolates had close relatives (≤22 substitutions) amongst animal and marine isolates, despite temporally and geographically distant sampling of these sources. Infection prevention measures are essential to limit transmission within human clinical settings and reduce disease burden. However, as colonisation often precedes infection, preventing transmission that leads to colonisation, e.g. transmission between animals and humans in the community, and in the food chain, could also be beneficial.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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