scholarly journals Genomic and Metabolic Profiling of Nonulosonic Acids in Vibrionaceae Reveal Biochemical Phenotypes of Allelic Divergence in Vibrio vulnificus

2011 ◽  
Vol 77 (16) ◽  
pp. 5782-5793 ◽  
Author(s):  
Amanda L. Lewis ◽  
Jean-Bernard Lubin ◽  
Shilpa Argade ◽  
Natasha Naidu ◽  
Biswa Choudhury ◽  
...  
Keyword(s):  
Vibrio Vulnificus ◽  
Hot Spot ◽  
Gene Clusters ◽  
Human Pathogens ◽  
Environmental Isolates ◽  
Content Type ◽  
The Family ◽  
Domains Of Life ◽  
Biochemical Analyses ◽  
And Function

ABSTRACTNonulosonic acids (NulOs) encompass a large group of structurally diverse nine-carbon backbone α-keto sugars widely distributed among the three domains of life. Mammals express a specialized version of NulOs called sialic acids, which are displayed in prominent terminal positions of cell surface and secreted glycoconjugates. Within bacteria, the ability to synthesize NulOs has been demonstrated in a number of human pathogens and is phylogenetically widespread. Here we examine the distribution, diversity, evolution, and function of NulO biosynthesis pathways in members of the familyVibrionaceae. Among 27 species ofVibrionaceaeexamined at the genomic level, 12 species containednabgene clusters. We document examples of duplication, divergence, horizontal transfer, and recombination ofnabgene clusters in differentVibrionaceaelineages. Biochemical analyses, including mass spectrometry, confirmed that many species do, in fact, produce di-N-acetylated NulOs. A library of clinical and environmental isolates ofVibrio vulnificusserved as a model for further investigation ofnaballele genotypes and levels of NulO expression. The data show that lineage I isolates produce about 20-fold higher levels of NulOs than lineage II isolates. Moreover,nabgene alleles found in a subset ofV. vulnificusclinical isolates express 40-fold higher levels of NulOs thannaballeles associated with environmental isolates. Taken together, the data implicate the familyVibrionaceaeas a “hot spot” of NulO evolution and suggest that these molecules may have diverse roles in environmental persistence and/or animal virulence.

scholarly journals Complete Genome Sequence of the Pathogenic Vibrio vulnificus Type Strain ATCC 27562

2017 ◽  
Vol 5 (35) ◽  
Author(s):  
Douglas B. Rusch ◽  
Dean A. Rowe-Magnus
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Vibrio Vulnificus ◽  
Foodborne Pathogen ◽  
The United States ◽  
Environmental Isolates ◽  
Content Type ◽  
Pathogenic Vibrio

ABSTRACT Vibrio vulnificus has the highest death rate and economic burden per case of any foodborne pathogen in the United States. A complete genome sequence of the type strain promotes comparative analyses with other clinical and environmental isolates, improving our understanding of this important human pathogen and successful environmental organism.

scholarly journals The Gene Cluster forpara-Nitrophenol Catabolism Is Responsible for 2-Chloro-4-Nitrophenol Degradation in Burkholderia sp. Strain SJ98

2014 ◽  
Vol 80 (19) ◽  
pp. 6212-6222 ◽  
Author(s):  
Jun Min ◽  
Jun-Jie Zhang ◽  
Ning-Yi Zhou
Keyword(s):  
Gene Cluster ◽  
Gene Knockout ◽  
Gene Clusters ◽  
Sole Source ◽  
Pcr Analysis ◽  
Content Type ◽  
Reverse Transcription Pcr ◽  
Biochemical Analyses ◽  
Nitrophenol Degradation

ABSTRACTBurkholderiasp. strain SJ98 (DSM 23195) utilizes 2-chloro-4-nitrophenol (2C4NP) orpara-nitrophenol (PNP) as a sole source of carbon and energy. Here, by genetic and biochemical analyses, a 2C4NP catabolic pathway different from those of all other 2C4NP utilizers was identified with chloro-1,4-benzoquinone (CBQ) as an intermediate. Reverse transcription-PCR analysis showed that all of thepnpgenes in thepnpABA1CDEFcluster were located in a single operon, which is significantly different from the genetic organization of all other previously reported PNP degradation gene clusters, in which the structural genes were located in three different operons. All of the Pnp proteins were purified to homogeneity as His-tagged proteins. PnpA, a PNP 4-monooxygenase, was found to be able to catalyze the monooxygenation of 2C4NP to CBQ. PnpB, a 1,4-benzoquinone reductase, has the ability to catalyze the reduction of CBQ to chlorohydroquinone. Moreover, PnpB is also able to enhance PnpA activityin vitroin the conversion of 2C4NP to CBQ. Genetic analyses indicated thatpnpAplays an essential role in the degradation of both 2C4NP and PNP by gene knockout and complementation. In addition to being responsible for the lower pathway of PNP catabolism, PnpCD, PnpE, and PnpF were also found to be likely involved in that of 2C4NP catabolism. These results indicated that the catabolism of 2C4NP and that of PNP share the same gene cluster in strain SJ98. These findings fill a gap in our understanding of the microbial degradation of 2C4NP at the molecular and biochemical levels.

scholarly journals N-Glycosylation of Haloferax volcanii Flagellins Requires Known Agl Proteins and Is Essential for Biosynthesis of Stable Flagella

2012 ◽  
Vol 194 (18) ◽  
pp. 4876-4887 ◽  
Author(s):  
Manuela Tripepi ◽  
Jason You ◽  
Sevcan Temel ◽  
Özlem Önder ◽  
Dustin Brisson ◽  
...  
Keyword(s):  
Gradient Centrifugation ◽  
Haloferax Volcanii ◽  
Content Type ◽  
Glycosylation Sites ◽  
Cscl Density Gradient ◽  
Domains Of Life ◽  
Covalently Linked ◽  
Glycosylation Pathway ◽  
A Minor ◽  
And Function

ABSTRACTN-glycosylation, a posttranslational modification required for the accurate folding and stability of many proteins, has been observed in organisms of all domains of life. Although the haloarchaeal S-layer glycoprotein was the first prokaryotic glycoprotein identified, little is known about the glycosylation of other haloarchaeal proteins. We demonstrate here that the glycosylation ofHaloferax volcaniiflagellins requires archaeal glycosylation (Agl) components involved in S-layer glycosylation and that the deletion of anyHfx. volcaniiaglgene impairs its swimming motility to various extents. A comparison of proteins in CsCl density gradient centrifugation fractions from supernatants of wild-typeHfx. volcaniiand deletion mutants lacking the oligosaccharyltransferase AglB suggests that when the Agl glycosylation pathway is disrupted, cells lack stable flagella, which purification studies indicate consist of a major flagellin, FlgA1, and a minor flagellin, FlgA2. Mass spectrometric analyses of FlgA1 confirm that its three predicted N-glycosylation sites are modified with covalently linked pentasaccharides having the same mass as that modifying its S-layer glycoprotein. Finally, the replacement of any of three predicted N-glycosylated asparagines of FlgA1 renders cells nonmotile, providing direct evidence for the first time that the N-glycosylation of archaeal flagellins is critical for motility. These results provide insight into the role that glycosylation plays in the assembly and function ofHfx. volcaniiflagella and demonstrate thatHfx. volcaniiflagellins are excellent reporter proteins for the study of haloarchaeal glycosylation processes.

scholarly journals Comparison of the Effects of Environmental Parameters on Growth Rates of Vibrio vulnificus Biotypes I, II, and III by Culture and Quantitative PCR Analysis

2011 ◽  
Vol 77 (12) ◽  
pp. 4200-4207 ◽  
Author(s):  
Eva Chase ◽  
Valerie J. Harwood
Keyword(s):  
Quantitative Pcr ◽  
Growth Rates ◽  
Environmental Changes ◽  
Vibrio Vulnificus ◽  
Environmental Parameters ◽  
Defined Medium ◽  
Pcr Analysis ◽  
Human Pathogens ◽  
Content Type ◽  
Specific Growth Rates

ABSTRACTVibrio vulnificusis a natural inhabitant of estuarine waters. The three known biotypes include (i) most human pathogens, (ii) primarily eel pathogens, and (iii) pathogens associated with fish and with human wound infections in Israel. Despite the frequently lethal consequences ofV. vulnificusinfections, the growth rates of the various biotypes and their response to environmental changes are not well characterized. We compared the specific growth rates (μ) of a representative of each biotype by culture and quantitative PCR (qPCR) analysis in a defined medium under varied pH, temperature, and salinity. Growth rates based on culturable concentrations were always higher than those based on qPCR estimates; however, both enumeration methods yielded comparable results on the influence of environmental factors on growth rates. Temperature (25°C, 30°C, 37°C), pH (7.0, 8.0), and salinity (5 to 40‰) all had significant effects on the μ of each biotype. Temperature had the greatest effect on the μ of biotype 1 (CMCP6), whereas salinity had the greatest effect on the μ of biotypes 2 (ATCC 33147) and 3 (302/99). The biotypes' growth rates varied significantly; biotype 1 grew most rapidly, while biotype 3 grew most slowly. The highest growth rates were achieved at 37°C, pH 7.0, and salinities of 15 to 30‰ (μ = 4.0, 2.9, and 2.4 generations h−1for biotypes 1, 2, and 3, respectively). Other strains of the biotypes yielded comparable results, suggesting that the physiological responses of the biotypes are differentially affected by parameters that are highly variable both in estuarine environments and between the free-living and pathogen states ofV. vulnificus.

scholarly journals Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation

2020 ◽  
Author(s):  
Isabel Johnston ◽  
Lucas J Osborn ◽  
Elizabeth A McManus ◽  
Anagha Kadam ◽  
Karlee B Schultz ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Biofilm Formation ◽  
Drug Targets ◽  
Gene Clusters ◽  
Essential Genes ◽  
Drug Resistant ◽  
Human Pathogens ◽  
Upec Strain ◽  
And Function ◽  
Key Steps

ABSTRACTAryl polyenes (APEs) are specialized polyunsaturated lipids that were identified in silico as the product of the most widespread family of bacterial biosynthetic gene clusters (BGCs). They are present in several Gram-negative host-associated bacteria, including multi-drug resistant human pathogens. Here, we characterize the biological function of APEs, focusing on the BGC from a uropathogenic Escherichia coli (UPEC) strain. We first perform a genetic deletion analysis to identify the essential genes required for APE biosynthesis. Next, we show that APEs function as fitness factors that increase protection from oxidative stress and contribute to biofilm formation. Together, our study highlights key steps in the APE biosynthesis pathway that can be explored as potential drug targets for complementary strategies to reduce fitness and prevent biofilm formation of multi-drug resistant pathogens.

scholarly journals The Divided Bacterial Genome: Structure, Function, and Evolution

2017 ◽  
Vol 81 (3) ◽  
Author(s):  
George C. diCenzo ◽  
Turlough M. Finan
Keyword(s):  
Meta Analysis ◽  
Bacterial Genome ◽  
Genome Structure ◽  
Dna Molecules ◽  
Human Pathogens ◽  
Genome Sequences ◽  
Bacterial Genomes ◽  
Content Type ◽  
A Genome ◽  
And Function

SUMMARY Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella, Vibrio, and Burkholderia. The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure.

scholarly journals Pseudouridine-FreeEscherichia coliRibosomes

2017 ◽  
Vol 200 (4) ◽  
Author(s):  
Michael O'Connor ◽  
Margus Leppik ◽  
Jaanus Remme
Keyword(s):  
Cell Growth ◽  
Functional Role ◽  
Ribosome Biogenesis ◽  
Content Type ◽  
E Coli ◽  
Pseudouridine Synthase ◽  
Domains Of Life ◽  
And Function ◽  
Critical Regions ◽  
Dependent Mechanism

ABSTRACTPseudouridine (Ψ) is present at conserved, functionally important regions in the ribosomal RNAs (rRNAs) from all three domains of life. Little, however, is known about the functions of Ψ modifications in bacterial ribosomes. AnEscherichia colistrain has been constructed in which all seven rRNA Ψ synthases have been inactivated and whose ribosomes are devoid of all Ψs. Surprisingly, this strain displays only minor defects in ribosome biogenesis and function, and cell growth is only modestly affected. This is in contrast to a strong requirement for Ψ in eukaryotic ribosomes and suggests divergent roles for rRNA Ψ modifications in these two domains.IMPORTANCEPseudouridine (Ψ) is the most abundant posttranscriptional modification in RNAs. In the ribosome, Ψ modifications are typically located at conserved, critical regions, suggesting they play an important functional role. In eukarya and archaea, rRNAs are modified by a single pseudouridine synthase (PUS) enzyme, targeted to rRNA via a snoRNA-dependent mechanism, while bacteria use multiple stand-alone PUS enzymes. Disruption of Ψ modification of rRNA in eukarya seriously impairs ribosome function and cell growth. We have constructed anE. colimultiple deletion strain lacking all Ψ modifications in rRNA. In contrast to the equivalent eukaryotic mutants, theE. colistrain is only modestly affected in growth, decoding, and ribosome biogenesis, indicating a differential requirement for Ψ modifications in these two domains.

scholarly journals Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses

2015 ◽  
Vol 90 (2) ◽  
pp. 659-669 ◽  
Author(s):  
Mang Shi ◽  
Xian-Dan Lin ◽  
Nikos Vasilakis ◽  
Jun-Hua Tian ◽  
Ci-Xiu Li ◽  
...  
Keyword(s):  
Host Range ◽  
Genome Size ◽  
Evolutionary History ◽  
Rna Viruses ◽  
Phenotypic Diversity ◽  
Genome Structure ◽  
Human Pathogens ◽  
Content Type ◽  
The Family ◽  
Vertebrate Hosts

ABSTRACTViruses of the familyFlaviviridaeare important pathogens of humans and other animals and are currently classified into four genera. To better understand their diversity, evolutionary history, and genomic flexibility, we used transcriptome sequencing (RNA-seq) to search for the viruses related to theFlaviviridaein a range of potential invertebrate and vertebrate hosts. Accordingly, we recovered the full genomes of five segmented jingmenviruses and 12 distant relatives of the knownFlaviviridae(“flavi-like” viruses) from a range of arthropod species. Although these viruses are highly divergent, they share a similar genomic plan and common ancestry with theFlaviviridaein the NS3 and NS5 regions. Remarkably, although these viruses fill in major gaps in the phylogenetic diversity of theFlaviviridae, genomic comparisons reveal important changes in genome structure, genome size, and replication/gene regulation strategy during evolutionary history. In addition, the wide diversity of flavi-like viruses found in invertebrates, as well as their deep phylogenetic positions, suggests that they may represent the ancestral forms from which the vertebrate-infecting viruses evolved. For the vertebrate viruses, we expanded the previously mammal-only pegivirus-hepacivirus group to include a virus from the graceful catshark (Proscyllium habereri), which in turn implies that these viruses possess a larger host range than is currently known. In sum, our data show that theFlaviviridaeinfect a far wider range of hosts and exhibit greater diversity in genome structure than previously anticipated.IMPORTANCEThe familyFlaviviridaeof RNA viruses contains several notorious human pathogens, including dengue virus, West Nile virus, and hepatitis C virus. To date, however, our understanding of the biodiversity and evolution of theFlaviviridaehas largely been directed toward vertebrate hosts and their blood-feeding arthropod vectors. Therefore, we investigated an expanded group of potential arthropod and vertebrate host species that have generally been ignored by surveillance programs. Remarkably, these species contained diverse flaviviruses and related viruses that are characterized by major changes in genome size and genome structure, such that these traits are more flexible than previously thought. More generally, these data suggest that arthropods may be the ultimate reservoir of theFlaviviridaeand related viruses, harboring considerable genetic and phenotypic diversity. In sum, this study revises the traditional view on the evolutionary history, host range, and genomic structures of a major group of RNA viruses.

scholarly journals Sialic Acid Catabolism and Transport Gene Clusters Are Lineage Specific in Vibrio vulnificus

2012 ◽  
Vol 78 (9) ◽  
pp. 3407-3415 ◽  
Author(s):  
Jean-Bernard Lubin ◽  
Joseph J. Kingston ◽  
Nityananda Chowdhury ◽  
E. Fidelma Boyd
Keyword(s):  
Sialic Acid ◽  
Carbon Source ◽  
Vibrio Vulnificus ◽  
Pathogenicity Island ◽  
Gene Clusters ◽  
Acid Uptake ◽  
Acid Transport ◽  
Content Type ◽  
Natural Isolates ◽  
Chromosome Ii

ABSTRACTSialic or nonulosonic acids are nine-carbon alpha ketosugars that are present in all vertebrate mucous membranes. Among bacteria, the ability to catabolize sialic acid as a carbon source is present mainly in pathogenic and commensal species of animals. Previously, it was shown that severalVibriospecies carry homologues of the genes required for sialic acid transport and catabolism, which are genetically linked. InVibrio choleraeon chromosome I, these genes are carried on theVibriopathogenicity island-2 region, which is confined to pathogenic isolates. We found that among the three sequencedVibrio vulnificusclinical strains, these genes are present on chromosome II and are not associated with a pathogenicity island. To determine whether the sialic acid transport (SAT) and catabolism (SAC) region is universally present withinV. vulnificus, we examined 67 natural isolates whose phylogenetic relationships are known. We found that the region was present predominantly among lineage I ofV. vulnificus, which is comprised mainly of clinical isolates. We demonstrate that the isolates that contain this region can catabolize sialic acid as a sole carbon source. Two putative transporters are genetically linked to the region inV. vulnificus, the tripartite ATP-independent periplasmic (TRAP) transporter SiaPQM and a component of an ATP-binding cassette (ABC) transporter. We constructed an in-frame deletion mutation insiaM, a component of the TRAP transporter, and demonstrate that this transporter is essential for sialic acid uptake in this species. Expression analysis of the SAT and SAC genes indicates that sialic acid is an inducer of expression. Overall, our study demonstrates that the ability to catabolize and transport sialic acid is predominately lineage specific inV. vulnificusand that the TRAP transporter is essential for sialic acid uptake.

scholarly journals Bioinformatic Mapping of Opine-Like Zincophore Biosynthesis in Bacteria

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Jacqueline R. Morey ◽  
Thomas E. Kehl-Fie
Keyword(s):  
Staphylococcus Aureus ◽  
Pseudomonas Aeruginosa ◽  
Small Molecules ◽  
Critical Role ◽  
Gene Clusters ◽  
Ecological Niches ◽  
Human Pathogens ◽  
Content Type ◽  
Marine Habitats ◽  
Animal Pathogens

ABSTRACT Zinc is an essential nutrient in biological systems due to its structural or catalytic requirement in proteins involved in diverse cellular processes. To meet this cellular demand, microbes must acquire sufficient zinc from their environment. However, many environments have low zinc availability. One of the mechanisms used by bacteria to acquire zinc is through the production of small molecules known as zincophores. Similar to bacterial siderophores used for iron uptake, zincophores are synthesized by the bacterium and exported and then reimported as zincophore-zinc complexes. Thus far, only four zincophores have been described, including two from the human pathogens Staphylococcus aureus and Pseudomonas aeruginosa, in which they play a critical role in zinc acquisition during infection, and one in a soil bacterium. To determine what other microbes may produce zincophores, we used bioinformatic analyses to identify new zincophore biosynthetic gene clusters (BGCs) and predict the diversity of molecules synthesized. Genome neighborhood network analysis identified approximately 250 unique zincophore-producing species from actinobacteria, firmicutes, proteobacteria, and fusobacteria. This indicates that zincophores are produced by diverse bacteria that inhabit a broad range of ecological niches. Many of the BGCs likely produce characterized zincophores, based on similarity to the characterized systems. However, this analysis also identified numerous BGCs that, based on the colocalization of additional modifying enzymes and sequence divergence of the biosynthetic enzymes, are likely to produce unique zincophores. Collectively, these findings provide a comprehensive understanding of the zincophore biosynthetic landscape that will be invaluable for future research on these important small molecules. IMPORTANCE Bacteria must acquire essential nutrients, including zinc, from their environment. For bacterial pathogens, this necessitates overcoming the host metal-withholding response known as nutritional immunity. A novel type of zinc uptake mechanism that involves the bacterial production of a small zinc-scavenging molecule was recently described in the human pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and Yersinia pestis, as well as the soil-associated bacterium Paenibacillus mucilaginosus. This suggests that zincophores may be important for zinc acquisition in diverse environments. In this study, we sought to identify other zincophore-producing bacteria using bioinformatics. We identified almost 250 unique zincophore-producing species, including human and animal pathogens, as well as isolates from soil, rhizosphere, plant, and marine habitats. Crucially, we observed diversity at the amino acid and gene organization levels, suggesting that many of these species are producing unique zincophores. Together, our findings highlight the importance of zincophores for a broad array of bacteria living in diverse environments.

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