scholarly journals Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities

2013 ◽  
Vol 79 (12) ◽  
pp. 3724-3733 ◽  
Author(s):  
Frank O. Aylward ◽  
Bradon R. McDonald ◽  
Sandra M. Adams ◽  
Alejandra Valenzuela ◽  
Rebeccah A. Schmidt ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
Genomic Analysis ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Glycoside Hydrolases ◽  
Content Type ◽  
Metabolic Versatility ◽  
Plasmid Recombination ◽  
Environmental Adaptations ◽  
Species Specific

ABSTRACTSphingomonads comprise a physiologically versatile group within theAlphaproteobacteriathat includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm thatSphingomonas,Sphingobium,Sphingopyxis, andNovosphingobiumare well-resolved monophyletic groups with the exception ofSphingomonassp. strain SKA58, which we propose belongs to the genusSphingobium. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible for their ability to degrade various recalcitrant aromatic compounds and polysaccharides, respectively. Many of these enzymes are encoded on megaplasmids, suggesting that they may be readily transferred between species. We also identified enzymes putatively used for the catabolism of sulfonate and nitroaromatic compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling.

scholarly journals Prevotella hominis sp. nov., isolated from human faeces

2020 ◽  
Vol 70 (8) ◽  
pp. 4767-4773 ◽  
Author(s):  
Jong-Shian Liou ◽  
Chien-Hsun Huang ◽  
Nao Ikeyama ◽  
Ai-Yun Lee ◽  
I-Ching Chen ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Genomic Analysis ◽  
Amino Acid Identity ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Link Type ◽  
Predominant Bacterium ◽  
Species Specific

A strictly anaerobic predominant bacterium, designated as strain gm001T, was isolated from a freshly voided faecal sample collected from a healthy Taiwanese adult. Cells were Gram-stain-negative rods, non-motile and non-spore-forming. Strain gm001T was identified as a member of the genus Prevotella , and a comparison of 16S rRNA and hsp60 gene sequences revealed sequence similarities of 98.5 and 93.3 %, respectively, demonstrating that it was most closely related to the type strain of Prevotella copri . Phylogenomic tree analysis indicated that the gm001T cluster is an independent lineage of P. copri DSM 18205T. The average nucleotide identity, digital DNA‒DNA hybridization and average amino acid identity values between strain gm001T and P. copri DSM 18205T were 80.9, 28.6 and 83.8 %, respectively, which were clearly lower than the species delineation thresholds. The species-specific genes of this novel species were also identified on the basis of pan-genomic analysis. The predominant menaquinones were MK-11 and MK-12, and the predominant fatty acids were anteiso-C15 : 0, C15 : 0 and iso-C15 : 0. Acetate and succinate were produced from glucose as metabolic end products. Taken together, the results indicate that strain gm001T represents a novel species of the genus Prevotella , for which the name Prevotella hominis sp. nov. is proposed. The type strain is gm001T (=BCRC 81118T=JCM 33280T).

scholarly journals Biology and Genome Sequence of Streptococcus mutans Phage M102AD

2012 ◽  
Vol 78 (7) ◽  
pp. 2264-2271 ◽  
Author(s):  
Allan L. Delisle ◽  
Ming Guo ◽  
Natalia I. Chalmers ◽  
Gerard J. Barcak ◽  
Geneviève M. Rousseau ◽  
...  
Keyword(s):  
Streptococcus Mutans ◽  
Genome Sequence ◽  
Gc Content ◽  
Genomic Analysis ◽  
Streptococcus Thermophilus ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Content Type ◽  
Close Relationship ◽  
Virion Structure

ABSTRACTM102AD is the new designation for aStreptococcus mutansphage described in 1993 as phage M102. This change was necessitated by the genome analysis of anotherS. mutansphage named M102, which revealed differences from the genome sequence reported here. Additional host range analyses confirmed thatS. mutansphage M102AD infects only a few serotype c strains. Phage M102AD adsorbed very slowly to its host, and it cannot adsorb to serotype e and f strains ofS. mutans. M102AD adsorption was blocked by c-specific antiserum. Phage M102AD also adsorbed equally well to heat-treated and trypsin-treated cells, suggesting carbohydrate receptors. Saliva and polysaccharide production did not inhibit plaque formation. The genome of this siphophage consisted of a linear, double-stranded, 30,664-bp DNA molecule, with a GC content of 39.6%. Analysis of the genome extremities indicated the presence of a 3′-overhangcossite that was 11 nucleotides long. Bioinformatic analyses identified 40 open reading frames, all in the same orientation. No lysogeny-related genes were found, indicating that phage M102AD is strictly virulent. No obvious virulence factor gene candidates were found. Twelve proteins were identified in the virion structure by mass spectrometry. Comparative genomic analysis revealed a close relationship betweenS. mutansphages M102AD and M102 as well as withStreptococcus thermophilusphages. This study also highlights the importance of conducting research with biological materials obtained from recognized microbial collections.

Two viruses that cause salivary gland hypertrophy in Glossina pallidipes and Musca domestica are related and form a distinct phylogenetic clade

2009 ◽  
Vol 90 (2) ◽  
pp. 334-346 ◽  
Author(s):  
Alejandra Garcia-Maruniak ◽  
Adly M. M. Abd-Alla ◽  
Tamer Z. Salem ◽  
Andrew G. Parker ◽  
Verena-Ulrike Lietze ◽  
...  
Keyword(s):  
Salivary Gland ◽  
Musca Domestica ◽  
Transcription Initiation ◽  
Genomic Analysis ◽  
Glossina Pallidipes ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Baculovirus Gene ◽  
Salivary Gland Hypertrophy

Glossina pallidipes and Musca domestica salivary gland hypertrophy viruses (GpSGHV and MdSGHV) replicate in the nucleus of salivary gland cells causing distinct tissue hypertrophy and reduction of host fertility. They share general characteristics with the non-occluded insect nudiviruses, such as being insect-pathogenic, having enveloped, rod-shaped virions, and large circular double-stranded DNA genomes. MdSGHV measures 65×550 nm and contains a 124 279 bp genome (∼44 mol% G+C content) that codes for 108 putative open reading frames (ORFs). GpSGHV, measuring 50×1000 nm, contains a 190 032 bp genome (28 mol% G+C content) with 160 putative ORFs. Comparative genomic analysis demonstrates that 37 MdSGHV ORFs have homology to 42 GpSGHV ORFs, as some MdSGHV ORFs have homology to two different GpSGHV ORFs. Nine genes with known functions (dnapol, ts, pif-1, pif-2, pif-3, mmp, p74, odv-e66 and helicase-2), a homologue of the conserved baculovirus gene Ac81 and at least 13 virion proteins are present in both SGHVs. The amino acid identity ranged from 19 to 39 % among ORFs. An (A/T/G)TAAG motif, similar to the baculovirus late promoter motif, was enriched 100 bp upstream of the ORF transcription initiation sites of both viruses. Six and seven putative microRNA sequences were found in MdSGHV and GpSGHV genomes, respectively. There was genome. Collinearity between the two SGHVs, but not between the SGHVs and the nudiviruses. Phylogenetic analysis of conserved genes clustered both SGHVs in a single clade separated from the nudiviruses and baculoviruses. Although MdSGHV and GpSGHV are different viruses, their pathology, host range and genome composition indicate that they are related.

scholarly journals Ultrastructural and Single-Cell-Level Characterization Reveals Metabolic Versatility in a Microbial Eukaryote Community from an Ice-Covered Antarctic Lake

2016 ◽  
Vol 82 (12) ◽  
pp. 3659-3670 ◽  
Author(s):  
Wei Li ◽  
Mircea Podar ◽  
Rachael M. Morgan-Kiss
Keyword(s):  
Food Web ◽  
Single Cell ◽  
Cell Sorting ◽  
Genomic Analysis ◽  
Microbial Interactions ◽  
Heterotrophic Nanoflagellates ◽  
Dry Valleys ◽  
Antarctic Lake ◽  
Content Type ◽  
Metabolic Versatility

ABSTRACTThe McMurdo Dry Valleys (MCM) of southern Victoria Land, Antarctica, harbor numerous ice-covered bodies of water that provide year-round liquid water oases for isolated food webs dominated by the microbial loop. Single-cell microbial eukaryotes (protists) occupy major trophic positions within this truncated food web, ranging from primary producers (e.g., chlorophytes, haptophytes, and cryptophytes) to tertiary predators (e.g., ciliates, dinoflagellates, and choanoflagellates). To advance the understanding of MCM protist ecology and the roles of MCM protists in nutrient and energy cycling, we investigated potential metabolic strategies and microbial interactions of key MCM protists isolated from a well-described lake (Lake Bonney). Fluorescence-activated cell sorting (FACS) of enrichment cultures, combined with single amplified genome/amplicon sequencing and fluorescence microscopy, revealed that MCM protists possess diverse potential metabolic capabilities and interactions. Two metabolically distinct bacterial clades (FlavobacteriaandMethylobacteriaceae) were independently associated with two key MCM lake microalgae (IsochrysisandChlamydomonas, respectively). We also report on the discovery of two heterotrophic nanoflagellates belonging to the Stramenopila supergroup, one of which lives as a parasite ofChlamydomonas, a dominate primary producer in the shallow, nutrient-poor layers of the lake.IMPORTANCESingle-cell eukaryotes called protists play critical roles in the cycling of organic matter in aquatic environments. In the ice-covered lakes of Antarctica, protists play key roles in the aquatic food web, providing the majority of organic carbon to the rest of the food web (photosynthetic protists) and acting as the major consumers at the top of the food web (predatory protists). In this study, we utilized a combination of techniques (microscopy, cell sorting, and genomic analysis) to describe the trophic abilities of Antarctic lake protists and their potential interactions with other microbes. Our work reveals that Antarctic lake protists rely on metabolic versatility for their energy and nutrient requirements in this unique and isolated environment.

scholarly journals Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains

2019 ◽  
Author(s):  
Mahoko Takahashi Ueda ◽  
Kirill Kryukov ◽  
Satomi Mitsuhashi ◽  
Hiroaki Mitsuhashi ◽  
Tadashi Imanishi ◽  
...  
Keyword(s):  
Host Species ◽  
Transcription Initiation ◽  
Protein Domains ◽  
Genomic Analysis ◽  
Cell Types ◽  
Endogenous Retroviruses ◽  
Open Reading Frames ◽  
Specific Expression ◽  
Mammalian Genomes ◽  
Species Specific

AbstractEndogenous retroviruses (ERVs) are remnants of ancient retroviral infections of mammalian germline cells. A large proportion of ERVs lose their open reading frames (ORFs), while others retain them and become exapted by the host species. However, it remains unclear what proportion of ERVs possess ORFs (ERV-ORFs), become transcribed, and serve as candidates for co-opted genes. Hence, we investigated characteristics of 176,401 ERV-ORFs containing retroviral-like protein domains (gag, pro, pol, and env) in 19 mammalian genomes. The fractions of ERVs possessing ORFs were overall small (∼0.15%) although they varied depending on domain types as well as species. The observed divergence of ERV-ORF from their consensus sequences suggested that a large proportion of ERV-ORFs either recently or anciently inserted themselves into mammalian genomes. Alternatively, very few ERVs lacking ORFs were found to exhibit similar divergence patterns. To identify ERV-ORFs transcribed as proteins, we compared ERV-ORFs with various multi-omics data including transcriptome data, trimethylation at histone H3 lysine 36, and transcription initiation sites from 2,834 cell types, and found 408 and 752 ERV-ORFs, accounting for 2-3% of all ERV-ORFs, with high transcriptional potential in humans and mice, respectively. Moreover, many of these ERV-ORFs with transcriptional potential were lineage-specific sequences exhibiting tissue-specific expression. These results suggest a possibility for the expression of uncharacterized functional genes containing ERV-ORFs hidden within mammalian genomes. Together, our analyses suggest that more ERV-ORFs may be co-opted in a host-species specific manner than we currently know, which are likely to have contributed to mammalian evolution and diversification.

scholarly journals Hyperthermophilic Thermotoga Species Differ with Respect to Specific Carbohydrate Transporters and Glycoside Hydrolases

2012 ◽  
Vol 78 (6) ◽  
pp. 1978-1986 ◽  
Author(s):  
Andrew D. Frock ◽  
Steven R. Gray ◽  
Robert M. Kelly
Keyword(s):  
Glucose Transporter ◽  
Open Reading Frames ◽  
The Other ◽  
Glycoside Hydrolases ◽  
Phosphotransferase System ◽  
Separate Species ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Sugar Transporters ◽  
Distinguishing Features

ABSTRACTFour hyperthermophilic members of the bacterial genusThermotoga(T. maritima,T. neapolitana,T. petrophila, andThermotogasp. strain RQ2) share a core genome of 1,470 open reading frames (ORFs), or about 75% of their genomes. Nonetheless, each species exhibited certain distinguishing features during growth on simple and complex carbohydrates that correlated with genomic inventories of specific ABC sugar transporters and glycoside hydrolases. These differences were consistent with transcriptomic analysis based on a multispecies cDNA microarray. Growth on a mixture of six pentoses and hexoses showed no significant utilization of galactose or mannose by any of the four species.T. maritimaandT. neapolitanaexhibited similar monosaccharide utilization profiles, with a strong preference for glucose and xylose over fructose and arabinose.Thermotogasp. strain RQ2 also used glucose and xylose, but was the only species to utilize fructose to any extent, consistent with a phosphotransferase system (PTS) specific for this sugar encoded in its genome.T. petrophilaused glucose to a significantly lesser extent than the other species. In fact, the XylR regulon was triggered by growth on glucose forT. petrophila, which was attributed to the absence of a glucose transporter (XylE2F2K2), otherwise present in the otherThermotogaspecies. This suggested thatT. petrophilaacquires glucose through the XylE1F1K1 transporter, which primarily serves to transport xylose in the other threeThermotogaspecies. The results here show that subtle differences exist among the hyperthermophilicThermotogaleswith respect to carbohydrate utilization, which supports their designation as separate species.

scholarly journals Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains

Mobile DNA ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Mahoko Takahashi Ueda ◽  
Kirill Kryukov ◽  
Satomi Mitsuhashi ◽  
Hiroaki Mitsuhashi ◽  
Tadashi Imanishi ◽  
...  
Keyword(s):  
Host Species ◽  
Protein Domains ◽  
Genomic Analysis ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Endogenous Retroviruses ◽  
Open Reading Frames ◽  
Consensus Sequences ◽  
Mammalian Genomes ◽  
Species Specific

Abstract Background Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of mammalian germline cells. A large proportion of ERVs lose their open reading frames (ORFs), while others retain them and become exapted by the host species. However, it remains unclear what proportion of ERVs possess ORFs (ERV-ORFs), become transcribed, and serve as candidates for co-opted genes. Results We investigated characteristics of 176,401 ERV-ORFs containing retroviral-like protein domains (gag, pro, pol, and env) in 19 mammalian genomes. The fractions of ERVs possessing ORFs were overall small (~ 0.15%) although they varied depending on domain types as well as species. The observed divergence of ERV-ORF from their consensus sequences showed bimodal distributions, suggesting that a large proportion of ERV-ORFs either recently, or anciently, inserted themselves into mammalian genomes. Alternatively, very few ERVs lacking ORFs were found to exhibit similar divergence patterns. To identify candidates for ERV-derived genes, we estimated the ratio of non-synonymous to synonymous substitution rates (dN/dS) for ERV-ORFs in human and non-human mammalian pairs, and found that approximately 42% of the ERV-ORFs showed dN/dS < 1. Further, using functional genomics data including transcriptome sequencing, we determined that approximately 9.7% of these selected ERV-ORFs exhibited transcriptional potential. Conclusions These results suggest that purifying selection operates on a certain portion of ERV-ORFs, some of which may correspond to uncharacterized functional genes hidden within mammalian genomes. Together, our analyses suggest that more ERV-ORFs may be co-opted in a host-species specific manner than we currently know, which are likely to have contributed to mammalian evolution and diversification.

scholarly journals Comparative Genomic Analysis of Acinetobacter oleivorans DR1 To Determine Strain-Specific Genomic Regions and Gentisate Biodegradation

2011 ◽  
Vol 77 (20) ◽  
pp. 7418-7424 ◽  
Author(s):  
Jaejoon Jung ◽  
Eugene L. Madsen ◽  
Che Ok Jeon ◽  
Woojun Park
Keyword(s):  
Metabolic Pathways ◽  
Genomic Analysis ◽  
Metal Resistance ◽  
Genomic Region ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Content Type ◽  
Large Size ◽  
Genomic Regions ◽  
Reading Frames

ABSTRACTThe comparative genomics ofAcinetobacter oleivoransDR1 assayed withA. baylyiADP1,A. calcoaceticusPHEA-2, andA. baumanniiATCC 17978 revealed that the incorporation of phage-related genomic regions and the absence of transposable elements have contributed to the large size (4.15 Mb) of the DR1 genome. A horizontally transferred genomic region and a higher proportion of transcriptional regulator- and signal peptide-coding genes were identified as characteristics of the DR1 genome. Incomplete glucose metabolism, metabolic pathways of aromatic compounds, biofilm formation, antibiotics and metal resistance, and natural competence genes were conserved in four compared genomes. Interestingly, only strain DR1 possesses gentisate 1,2-dioxygenase (nagI) and grows on gentisate, whereas other species cannot. Expression of thenagIgene was upregulated during gentisate utilization, and four downstream open reading frames (ORFs) were cotranscribed, supporting the notion that gentisate metabolism is a unique characteristic of strain DR1. The genomic analysis of strain DR1 provides additional insights into the function, ecology, and evolution ofAcinetobacterspecies.

scholarly journals Complete Genome Sequence of Virulence-Enhancing Siphophage VHS1 from Vibrio harveyi

2012 ◽  
Vol 78 (8) ◽  
pp. 2790-2796 ◽  
Author(s):  
Krit Khemayan ◽  
Anuphap Prachumwat ◽  
Burachai Sonthayanon ◽  
Aungkul Intaraprasong ◽  
Siriporn Sriurairatana ◽  
...  
Keyword(s):  
Vibrio Harveyi ◽  
Protein A ◽  
Penaeus Monodon ◽  
Open Reading Frames ◽  
Tape Measure Protein ◽  
Content Type ◽  
Software Analysis ◽  
Dna Strand ◽  
Species Specific ◽  
Head Protein

ABSTRACTVibrio harveyisiphophage 1 (VHS1) is a tailed phage with an icosahedral head of approximately 66 nm in diameter and an unornamented, flexible tail of approximately 153 nm in length. WhenVibrio harveyi1114GL is lysogenized with VHS1, its virulence for the black tiger shrimp (Penaeus monodon) increases by more than 100 times, and this coincides with production of a toxin(s) associated with shrimp hemocyte agglutination. Curiously, the lysogen does not show increased virulence for the whiteleg shrimp (Penaeus[Litopenaeus]vannamei). Here we present and annotate the complete, circular genome of VHS1 (81,509 kbp; GenBank accession numberJF713456). By software analysis, the genome contains 125 putative open reading frames (ORFs), all of which appear to be located on the same DNA strand, similar to the case for many other bacteriophages. Most of the putative ORFs show no significant homology to known sequences in GenBank. Notable exceptions are ORFs for a putative DNA polymerase and putative phage structural proteins, including a portal protein, a phage tail tape measure protein, and a phage head protein. The last protein was identified as a component of the species-specific toxin mixture described above as being associated with agglutination of hemocytes fromP. monodon.

scholarly journals Investigating the Function of an Arabinan Utilization Locus Isolated from a Termite Gut Community

2014 ◽  
Vol 81 (1) ◽  
pp. 31-39 ◽  
Author(s):  
Grégory Arnal ◽  
Géraldine Bastien ◽  
Nelly Monties ◽  
Anne Abot ◽  
Véronique Anton Leberre ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Plant Biomass ◽  
Bioinformatic Analysis ◽  
Open Reading Frames ◽  
Glycoside Hydrolases ◽  
Functional Screening ◽  
Content Type ◽  
Termite Gut ◽  
Pentose Sugar

ABSTRACTBiocatalysts are essential for the development of bioprocesses efficient for plant biomass degradation. Previously, a metagenomic clone containing DNA from termite gut microbiota was pinpointed in a functional screening that revealed the presence of arabinofuranosidase activity. Subsequent genetic and bioinformatic analysis revealed that the DNA fragment belonged to a member of the genusBacteroidesand encoded 19 open reading frames (ORFs), and annotation suggested the presence of hypothetical transporter and regulator proteins and others involved in the catabolism of pentose sugar. In this respect and considering the phenotype of the metagenomic clone, it was noted that among the ORFs, there are four putative arabinose-specific glycoside hydrolases, two from family GH43 and two from GH51. In this study, a thorough bioinformatics analysis of the metagenomic clone gene cluster has been performed and the four aforementioned glycoside hydrolases have been characterized. Together, the results provide evidence that the gene cluster is a polysaccharide utilization locus dedicated to the breakdown of the arabinan component in pectin and related substrates. Characterization of the two GH43 and the two GH51 glycoside hydrolases has revealed that each of these enzymes displays specific catalytic capabilities and that when these are combined the enzymes act synergistically, increasing the efficiency of arabinan degradation.

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