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Nature Microbiology Dec 2020Photorhabdus and Xenorhabdus species have mutualistic associations with nematodes and an entomopathogenic stage in their life cycles. In both stages, numerous...
Photorhabdus and Xenorhabdus species have mutualistic associations with nematodes and an entomopathogenic stage in their life cycles. In both stages, numerous specialized metabolites are produced that have roles in symbiosis and virulence. Although regulators have been implicated in the regulation of these specialized metabolites, how small regulatory RNAs (sRNAs) are involved in this process is not clear. Here, we show that the Hfq-dependent sRNA, ArcZ, is required for specialized metabolite production in Photorhabdus and Xenorhabdus. We discovered that ArcZ directly base-pairs with the mRNA encoding HexA, which represses the expression of specialized metabolite gene clusters. In addition to specialized metabolite genes, we show that the ArcZ regulon affects approximately 15% of all transcripts in Photorhabdus and Xenorhabdus. Thus, the ArcZ sRNA is crucial for specialized metabolite production in Photorhabdus and Xenorhabdus species and could become a useful tool for metabolic engineering and identification of commercially relevant natural products.
Topics: Animals; Biological Products; Gene Expression Regulation, Bacterial; Insecta; Nematoda; Photorhabdus; RNA, Bacterial; RNA, Small Untranslated; Symbiosis; Virulence; Xenorhabdus
PubMed: 33139881
DOI: 10.1038/s41564-020-00797-5 -
Current Microbiology Jun 2024One Gram-negative, rod-shaped bacterial strain, isolated from an undescribed Heterorhabditis entomopathogenic nematode species was characterized to determine its...
One Gram-negative, rod-shaped bacterial strain, isolated from an undescribed Heterorhabditis entomopathogenic nematode species was characterized to determine its taxonomic position. The 16S rRNA gene sequences indicate that it belongs to the class Gammaproteobacteria, to the family Morganellaceae, to the genus Photorhabdus, and likely represents a novel bacterial species. This strain, designated here as CRI-LC, was therefore molecularly, biochemically, and morphologically characterized to describe the novel bacterial species. Phylogenetic reconstructions using 16S rRNA gene sequences show that CRI-LC is closely related to P. laumondii subsp. laumondii TT01 and to P. laumondii subsp. clarkei BOJ-47. The 16rRNA gene sequences between CRI-LC and P. laumondii subsp. laumondii TT01 are 99.1% identical, and between CRI-LC and P. laumondii subsp. clarkei BOJ-47 are 99.2% identical. Phylogenetic reconstructions using whole genome sequences show that CRI-LC is closely related to P. laumondii subsp. laumondii TT01 and to P. laumondii subsp. clarkei BOJ-47. Moreover, digital DNA-DNA hybridization (dDDH) values between CRI-LC and its two relative species P. laumondii subsp. laumondii TT01 and P. laumondii subsp. clarkei BOJ-47 are 65% and 63%, respectively. In addition, we observed that average nucleotide identity (ANI) values between CRI-LC and its two relative species P. laumondii subsp. laumondii TT01 and P. laumondii subsp. clarkei BOJ-47 are 95.8% and 95.5%, respectively. These values are below the 70% dDDH and the 95-96% ANI divergence thresholds that delimits prokaryotic species. Based on these genomic divergence values, and the phylogenomic separation, we conclude that CRI-LC represents a novel bacterial species, for which we propose the name Photorhabdus africana sp. nov. with CRI-LC (= CCM 9390 = CCOS 2112) as the type strain. The following biochemical tests allow to differentiate P. africana sp. nov. CRI-LC from other species of the genus, including its more closely related taxa: β-Galactosidase, citrate utilization, urease and tryptophan deaminase activities, indole and acetoin production, and glucose and inositol oxidation. Our study contributes to a better understanding of the taxonomy and biodiversity of this important bacterial group with great biotechnological and agricultural potential.
Topics: Phylogeny; Photorhabdus; Animals; RNA, Ribosomal, 16S; DNA, Bacterial; Rhabditoidea; Sequence Analysis, DNA; Bacterial Typing Techniques
PubMed: 38910178
DOI: 10.1007/s00284-024-03744-3 -
Molecular Microbiology Oct 2009
Topics: Bacillus subtilis; Genomics; History, 20th Century; History, 21st Century; Legionella pneumophila; Microbiology; Molecular Biology; Photorhabdus
PubMed: 19843231
DOI: 10.1111/j.1365-2958.2009.06881.x -
Cellular Microbiology Jul 2009Invertebrate animal models are experimentally tractable and have immunity and disease symptoms that mirror those of vertebrates. Therefore they are of particular utility... (Review)
Review
Invertebrate animal models are experimentally tractable and have immunity and disease symptoms that mirror those of vertebrates. Therefore they are of particular utility in understanding fundamental aspects of pathogenesis. Indeed, artificial models using human pathogens and invertebrate hosts have revealed conserved and novel molecular mechanisms of bacterial infection and host immune responses. Additional insights may be gained from investigating interactions between invertebrates and pathogens they encounter in their natural environments. For example, enteric bacteria in the genera Photorhabdus and Xenorhabdus are pathogens of insects that also mutualistically associate with nematodes in the genera Heterorhabditis and Steinernema respectively. These bacteria serve as models to understand naturally occurring symbiotic associations that result in disease in or benefit for animals. Xenorhabdus nematophila is the best-studied species of its genus with regard to the molecular mechanisms of its symbiotic associations. In this review, we summarize recent advances in understanding X. nematophila-host interactions. We emphasize regulatory cascades involved in coordinating transitions between various stages of the X. nematophila life cycle: infection, reproduction and transmission.
Topics: Animals; Disease Models, Animal; Gene Expression Regulation, Bacterial; Gram-Negative Bacterial Infections; Host-Pathogen Interactions; Humans; Rhabditida; Rhabditoidea; Symbiosis; Virulence; Xenorhabdus
PubMed: 19374654
DOI: 10.1111/j.1462-5822.2009.01322.x -
Biology Feb 2022(Lepidoptera: Lycaenidae) and (Lepidoptera: Pyralidae) are the key pests of pomegranates in Saudi Arabia that are managed mainly using broad-spectrum pesticides....
Isolation, Identification, and Biocontrol Potential of Entomopathogenic Nematodes and Associated Bacteria against (Lepidoptera: Lycaenidae) and (Lepidoptera: Pyralidae).
(Lepidoptera: Lycaenidae) and (Lepidoptera: Pyralidae) are the key pests of pomegranates in Saudi Arabia that are managed mainly using broad-spectrum pesticides. Interactions between the entomopathogenic nematodes (EPNs) Steinernematids, and Heterorhabditids, and their entomopathogenic bacterial symbionts (EPBs) have long been considered monoxenic 2-partner associations responsible for killing insects and, therefore, are widely used in insect pest biocontrol. However, there are limited reports identifying such organisms in Taif, Saudi Arabia. The current study aimed to identify the EPNs and their associated bacteria isolated from Taif, Saudi Arabia, and evaluate their biocontrol potential on third instar larvae of and under laboratory conditions. A total of 35 EPN isolates belonging to (20) and (15) were recovered from 320 soil samples. Twenty-six isolates of symbiotic or associated bacteria were isolated from EPNs and molecularly identified as (6 isolates), (4 isolates), (7), or (9). A pathogenicity assay revealed that spp. were more virulent than spp. against the two pomegranate insects, with LC values of 18.5 and 13.6 infective juveniles (IJs)/larva of for spp. and 52 and 32.4 IJs/larva of for spp. at 48 and 72 h post-treatment, respectively. Moreover, LC values of 9 and 6.6 IJs/larva ( spp.) and 34.4 and 26.6 IJs/larva ( spp.) were recorded for larvae at 48 and 72 h post-treatment. In addition, the EPB CQ1, isolated from spp., surpassed SJ10, associated with spp., in their ability to kill or larvae within 6 h post-application, resulting in 100% mortality in both insects after 24 and 48 h of exposure. We conclude that either application of EPNs' IJs or their associated EPBs could serve as potential biocontrol agents for and .
PubMed: 35205161
DOI: 10.3390/biology11020295 -
Frontiers in Cellular and Infection... 2014Bacteria communicate via small diffusible molecules to mediate group-coordinated behavior, a process designated as quorum sensing. The basic molecular quorum sensing...
Bacteria communicate via small diffusible molecules to mediate group-coordinated behavior, a process designated as quorum sensing. The basic molecular quorum sensing system of Gram-negative bacteria consists of a LuxI-type autoinducer synthase producing acyl-homoserine lactones (AHLs) as signaling molecules, and a LuxR-type receptor detecting the AHLs to control expression of specific genes. However, many proteobacteria possess one or more unpaired LuxR-type receptors that lack a cognate LuxI-like synthase, referred to as LuxR solos. The enteric and insect pathogenic bacteria of the genus Photorhabdus harbor an extraordinarily high number of LuxR solos, more than any other known bacteria, and all lack a LuxI-like synthase. Here, we focus on the presence and the different types of LuxR solos in the three known Photorhabdus species using bioinformatics analyses. Generally, the N-terminal signal-binding domain (SBD) of LuxR-type receptors sensing AHLs have a motif of six conserved amino acids that is important for binding and specificity of the signaling molecule. However, this motif is altered in the majority of the Photorhabdus-specific LuxR solos, suggesting the use of other signaling molecules than AHLs. Furthermore, all Photorhabdus species contain at least one LuxR solo with an intact AHL-binding motif, which might allow the ability to sense AHLs of other bacteria. Moreover, all three species have high AHL-degrading activity caused by the presence of different AHL-lactonases and AHL-acylases, revealing a high quorum quenching activity against other bacteria. However, the majority of the other LuxR solos in Photorhabdus have a N-terminal so-called PAS4-domain instead of an AHL-binding domain, containing different amino acid motifs than the AHL-sensors, which potentially allows the recognition of a highly variable range of signaling molecules that can be sensed apart from AHLs. These PAS4-LuxR solos are proposed to be involved in host sensing, and therefore in inter-kingdom signaling. Overall, Photorhabdus species are perfect model organisms to study bacterial communication via LuxR solos and their role for a symbiotic and pathogenic life style.
Topics: Acyl-Butyrolactones; Amino Acid Motifs; Carboxylic Ester Hydrolases; Conserved Sequence; Genome, Bacterial; Photorhabdus; Phylogeny; Position-Specific Scoring Matrices; Protein Binding; Protein Interaction Domains and Motifs; Quorum Sensing; Repressor Proteins; Signal Transduction; Trans-Activators
PubMed: 25478328
DOI: 10.3389/fcimb.2014.00166 -
PLoS Computational Biology Feb 2021The vast expansion of protein sequence databases provides an opportunity for new protein design approaches which seek to learn the sequence-function relationship...
The vast expansion of protein sequence databases provides an opportunity for new protein design approaches which seek to learn the sequence-function relationship directly from natural sequence variation. Deep generative models trained on protein sequence data have been shown to learn biologically meaningful representations helpful for a variety of downstream tasks, but their potential for direct use in the design of novel proteins remains largely unexplored. Here we show that variational autoencoders trained on a dataset of almost 70000 luciferase-like oxidoreductases can be used to generate novel, functional variants of the luxA bacterial luciferase. We propose separate VAE models to work with aligned sequence input (MSA VAE) and raw sequence input (AR-VAE), and offer evidence that while both are able to reproduce patterns of amino acid usage characteristic of the family, the MSA VAE is better able to capture long-distance dependencies reflecting the influence of 3D structure. To confirm the practical utility of the models, we used them to generate variants of luxA whose luminescence activity was validated experimentally. We further showed that conditional variants of both models could be used to increase the solubility of luxA without disrupting function. Altogether 6/12 of the variants generated using the unconditional AR-VAE and 9/11 generated using the unconditional MSA VAE retained measurable luminescence, together with all 23 of the less distant variants generated by conditional versions of the models; the most distant functional variant contained 35 differences relative to the nearest training set sequence. These results demonstrate the feasibility of using deep generative models to explore the space of possible protein sequences and generate useful variants, providing a method complementary to rational design and directed evolution approaches.
Topics: Algorithms; Computational Biology; Computer Simulation; Escherichia coli; Machine Learning; Neural Networks, Computer; Oxidoreductases; Photorhabdus; Proteins; Recombinant Proteins; Reproducibility of Results; Solubility
PubMed: 33635868
DOI: 10.1371/journal.pcbi.1008736 -
Insects Oct 2018causes considerable economic damage to small and thin-skinned fruits including cherry, blueberry, raspberry, grape and strawberry. Since it attacks fruits at the...
causes considerable economic damage to small and thin-skinned fruits including cherry, blueberry, raspberry, grape and strawberry. Since it attacks fruits at the ripening stage, the use of chemical pesticides is limited due to the high risk of residues on fruit. Biological control is thus expected to play an essential role in managing this pest. The Gram-negative bacterium, and its symbiotic spp. nematode have been shown to be highly pathogenic to insects, with a potential for replacing pesticides to suppress several pests. Insecticidal activity of at different bacterial cell concentrations and its cell-free supernatant were assessed against third-instar larvae and pupae of under laboratory conditions. suspensions had a significant oral and contact toxicity on larvae and pupae, with mortalities up to of 70⁻100% 10 days after treatment. Cell-free supernatant in the diet also doubled mortality rates of feeding larvae. Our results suggest that may be a promising candidate for biological control of , and its use in integrated pest management (IPM) programs is discussed.
PubMed: 30360545
DOI: 10.3390/insects9040148 -
Insects Nov 2021The European grapevine moth (EGVM) (Lepidoptera: Tortricidae) is a relevant pest in the Palearctic region vineyards and is present in the Americas. Their management...
The European grapevine moth (EGVM) (Lepidoptera: Tortricidae) is a relevant pest in the Palearctic region vineyards and is present in the Americas. Their management using biological control agents and environmentally friendly biotechnical tools would reduce intensive pesticide use. The entomopathogenic nematodes (EPNs) in the families Steinernematidae and Heterorhabditidae are well-known virulent agents against arthropod pests thanks to symbiotic bacteria in the genera and (respectively) that produce natural products with insecticidal potential. Novel technological advances allow field applications of EPNs and those bioactive compounds as powerful bio-tools against aerial insect pests. This study aimed to determine the viability of four EPN species (, , , and ) as biological control agents against EGVM larval instars (L1, L3, and L5) and pupae. Additionally, the bioactive compounds from their four symbiotic bacteria (, , , and subsp. respectively) were tested as unfiltered ferment (UF) and cell-free supernatant (CFS) against the EGVM larval instars L1 and L3. All of the EPN species showed the capability of killing EGVM during the larval and pupal stages, particularly (mortalities of ~50% for L1 and >75% for L3 and L5 in only two days), followed by efficacy by . Similarly, the bacterial bioactive compounds produced higher larval mortality at three days against L1 (>90%) than L3 (~50%), making the application of UF more virulent than the application of CFS. Our findings indicate that both steinernematid species and their symbiotic bacterial bioactive compounds could be considered for a novel agro-technological approach to control in vineyards. Further research into co-formulation with adjuvants is required to expand their viability when implemented for aboveground grapevine application.
PubMed: 34821833
DOI: 10.3390/insects12111033 -
Marine Drugs Dec 2017In aquaculture, shrimp farming is a popular field. The benefits of shrimp farming include a relatively short grow-out time, high sale price, and good cost recovery.... (Review)
Review
In aquaculture, shrimp farming is a popular field. The benefits of shrimp farming include a relatively short grow-out time, high sale price, and good cost recovery. However, outbreaks of serious diseases inflict serious losses, and acute hepatopancreatic necrosis disease (AHPND) is an emerging challenge to this industry. In South American white shrimp () and grass shrimp (), this disease has a 70-100% mortality. The pathogenic agent of AHPND is a specific strain of which contains PirA and PirB toxins encoded in the pVA1 plasmid. PirA and PirB have been shown to cause the typical histological symptoms of AHPND in infected shrimps, and in this review, we will focus on our structural understanding of these toxins. By analyzing their structures, a possible cytotoxic mechanism, as well as strategies for anti-AHPND drug design, is proposed.
Topics: Animals; Aquaculture; Aquatic Organisms; Bacterial Proteins; Penaeidae; Toxins, Biological; Vibrio parahaemolyticus
PubMed: 29194352
DOI: 10.3390/md15120373