Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella

Microbiology ◽  
2003 ◽  
Vol 149 (11) ◽  
pp. 3051-3072 ◽  
Author(s):  
Christopher R. Peabody ◽  
Yong Joon Chung ◽  
Ming-Ren Yen ◽  
Dominique Vidal-Ingigliardi ◽  
Anthony P. Pugsley ◽  
...  
Keyword(s):  
Structural Characteristics ◽  
Phylogenetic Analyses ◽  
Klebsiella Oxytoca ◽  
Sequence Divergence ◽  
Type Ii ◽  
Type Iv ◽  
The Family ◽  
Uniform Function ◽  
Duplication Events ◽  
The Individual

Homologues of the protein constituents of the Klebsiella pneumoniae (Klebsiella oxytoca) type II secreton (T2S), the Pseudomonas aeruginosa type IV pilus/fimbrium biogenesis machinery (T4P) and the Methanococcus voltae flagellum biogenesis machinery (Fla) have been identified. Known constituents of these systems include (1) a major prepilin (preflagellin), (2) several minor prepilins (preflagellins), (3) a prepilin (preflagellin) peptidase/methylase, (4) an ATPase, (5) a multispanning transmembrane (TM) protein, (6) an outer-membrane secretin (lacking in Fla) and (7) several functionally uncharacterized envelope proteins. Sequence and phylogenetic analyses led to the conclusion that, although many of the protein constituents are probably homologous, extensive sequence divergence during evolution clouds this homology so that a common ancestry can be established for all three types of systems for only two constituents, the ATPase and the TM protein. Sequence divergence of the individual T2S constituents has occurred at characteristic rates, apparently without shuffling of constituents between systems. The same is probably also true for the T4P and Fla systems. The family of ATPases is much larger than the family of TM proteins, and many ATPase homologues function in capacities unrelated to those considered here. Many phylogenetic clusters of the ATPases probably exhibit uniform function. Some of these have a corresponding TM protein homologue although others probably function without one. It is further shown that proteins that compose the different phylogenetic clusters in both the ATPase and the TM protein families exhibit unique structural characteristics that are of probable functional significance. The TM proteins are shown to have arisen by at least two dissimilar intragenic duplication events, one in the bacterial kingdom and one in the archaeal kingdom. The archaeal TM proteins are twice as large as the bacterial TM proteins, suggesting an oligomeric structure for the latter.

scholarly journals Multiple Types of Novel Enteric Bopiviruses (Picornaviridae) with the Possibility of Interspecies Transmission Identified from Cloven-Hoofed Domestic Livestock (Ovine, Caprine and Bovine) in Hungary

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 66
Author(s):  
Zoltán László ◽  
Péter Pankovics ◽  
Gábor Reuter ◽  
Attila Cságola ◽  
Ádám Bálint ◽  
...  
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Interspecies Transmission ◽  
Background Information ◽  
Type Ii ◽  
Rt Pcr ◽  
Faecal Samples ◽  
The Family ◽  
Domestic Livestock

Most picornaviruses of the family Picornaviridae are relatively well known, but there are certain “neglected” genera like Bopivirus, containing a single uncharacterised sequence (bopivirus A1, KM589358) with very limited background information. In this study, three novel picornaviruses provisionally called ovipi-, gopi- and bopivirus/Hun (MW298057-MW298059) from enteric samples of asymptomatic ovine, caprine and bovine respectively, were determined using RT-PCR and dye-terminator sequencing techniques. These monophyletic viruses share the same type II-like IRES, NPGP-type 2A, similar genome layout (4-3-4) and cre-localisations. Culture attempts of the study viruses, using six different cell lines, yielded no evidence of viral growth in vitro. Genomic and phylogenetic analyses show that bopivirus/Hun of bovine belongs to the species Bopivirus A, while the closely related ovine-origin ovipi- and caprine-origin gopivirus could belong to a novel species “Bopivirus B” in the genus Bopivirus. Epidemiological investigation of N = 269 faecal samples of livestock (ovine, caprine, bovine, swine and rabbit) from different farms in Hungary showed that bopiviruses were most prevalent among <12-month-old ovine, caprine and bovine, but undetectable in swine and rabbit. VP1 capsid-based phylogenetic analyses revealed the presence of multiple lineages/genotypes, including closely related ovine/caprine strains, suggesting the possibility of ovine–caprine interspecies transmission of certain bopiviruses.

scholarly journals Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae)

2009 ◽  
Vol 83 (21) ◽  
pp. 11233-11243 ◽  
Author(s):  
Stephanie D. Friedman ◽  
Fred J. Genthner ◽  
Jennifer Gentry ◽  
Mark D. Sobsey ◽  
Jan Vinjé
Keyword(s):  
Complete Genome ◽  
Catalytic Domain ◽  
Phylogenetic Analyses ◽  
Detailed Knowledge ◽  
Genome Sequences ◽  
Virus Family ◽  
Sequence Identity ◽  
The Family ◽  
The Individual ◽  
Male Specific

ABSTRACT Male-specific single-stranded RNA (FRNA) coliphages belong to the family Leviviridae. They are classified into two genera (Levivirus and Allolevivirus), which can be subdivided into four genogroups (genogroups I and II in Levivirus and genogroups III and IV in Allolevivirus). Relatively few strains have been completely characterized, and hence, a detailed knowledge of this virus family is lacking. In this study, we sequenced and characterized the complete genomes of 19 FRNA strains (10 Levivirus strains and 9 Allolevivirus strains) and compared them to the 11 complete genome sequences available in GenBank. Nucleotide similarities among strains of Levivirus genogroups I and II were 75% to 99% and 83 to 94%, respectively, whereas similarities among strains of Allolevivirus genogroups III and IV ranged from 70 to 96% and 75 to 95%, respectively. Although genogroup I strain fr and genogroup III strains MX1 and M11 share only 70 to 78% sequence identity with strains in their respective genogroups, phylogenetic analyses of the complete genome and the individual genes suggest that strain fr should be grouped in Levivirus genogroup I and that the MX1 and M11 strains belong in Allolevivirus genogroup III. Strains within each genus share >50% sequence identity, whereas between the two genera, strains have <40% nucleotide sequence identity. Overall, amino acid composition, nucleotide similarities, and replicase catalytic domain location contributed to phylogenetic assignments. A conserved eight-nucleotide signature at the 3′ end of the genome distinguishes leviviruses (5′ ACCACCCA 3′) from alloleviviruses (5′ TCCTCCCA 3′).

scholarly journals The eukaryotic MEP-pathway genes are evolutionarily conserved and originated from Chlaymidia and cyanobacteria

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Liping Zeng ◽  
Katayoon Dehesh
Keyword(s):  
Phylogenetic Analyses ◽  
Single Copy ◽  
Mep Pathway ◽  
Syntenic Block ◽  
Bioinformatics Analyses ◽  
Expression Levels ◽  
Methylerythritol Phosphate ◽  
Duplication Events ◽  
History Of ◽  
The Individual

Abstract Background Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes. Results Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development. Conclusion Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.

scholarly journals The MEP-pathway genes are polyphyletic origin and evolutionary conserved

2020 ◽  
Author(s):  
Liping Zeng ◽  
Katayoon Dehesh
Keyword(s):  
Phylogenetic Analyses ◽  
Single Copy ◽  
Mep Pathway ◽  
Syntenic Block ◽  
Bioinformatics Analyses ◽  
Expression Levels ◽  
Duplication Events ◽  
History Of ◽  
The Individual ◽  
Comprehensive Study

Abstract BackgroundIsoprenoids are amongst the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol dicyclophosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes.ResultsHere, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development. ConclusionCollectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.

scholarly journals Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae

2021 ◽  
Vol 12 ◽  
Author(s):  
Sangita Karki ◽  
Mohammad Moniruzzaman ◽  
Frank O. Aylward
Keyword(s):  
African Swine Fever Virus ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
African Swine Fever ◽  
Salient Feature ◽  
Metagenomic Data ◽  
Genome Comparison ◽  
Marker Genes ◽  
Environmental Distribution ◽  
The Family

The family Asfarviridae is a group of nucleo-cytoplasmic large DNA viruses (NCLDVs) of which African swine fever virus (ASFV) is well-characterized. Recently the discovery of several Asfarviridae members other than ASFV has suggested that this family represents a diverse and cosmopolitan group of viruses, but the genomics and distribution of this family have not been studied in detail. To this end we analyzed five complete genomes and 35 metagenome-assembled genomes (MAGs) of viruses from this family to shed light on their evolutionary relationships and environmental distribution. The Asfarvirus MAGs derive from diverse marine, freshwater, and terrestrial habitats, underscoring the broad environmental distribution of this family. We present phylogenetic analyses using conserved marker genes and whole-genome comparison of pairwise average amino acid identity (AAI) values, revealing a high level of genomic divergence across disparate Asfarviruses. Further, we found that Asfarviridae genomes encode genes with diverse predicted metabolic roles and detectable sequence homology to proteins in bacteria, archaea, and eukaryotes, highlighting the genomic chimerism that is a salient feature of NCLDV. Our read mapping from Tara oceans metagenomic data also revealed that three Asfarviridae MAGs were present in multiple marine samples, indicating that they are widespread in the ocean. In one of these MAGs we identified four marker genes with &gt; 95% AAI to genes sequenced from a virus that infects the dinoflagellate Heterocapsa circularisquama (HcDNAV). This suggests a potential host for this MAG, which would thereby represent a reference genome of a dinoflagellate-infecting giant virus. Together, these results show that Asfarviridae are ubiquitous, comprise similar sequence divergence as other NCLDV families, and include several members that are widespread in the ocean and potentially infect ecologically important protists.

Evolution and structural diversification of hyperpolarization-activated cyclic nucleotide-gated channel genes

2007 ◽  
Vol 29 (3) ◽  
pp. 231-245 ◽  
Author(s):  
Heather A. Jackson ◽  
Christian R. Marshall ◽  
Eric A. Accili
Keyword(s):  
Cyclic Nucleotide ◽  
Phylogenetic Analyses ◽  
Critical Role ◽  
Hcn Channels ◽  
Ancestral Gene ◽  
Conserved Sequence ◽  
Gated Channel ◽  
Duplication Events ◽  
The Individual ◽  
And Function

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are members of the voltage-gated channel superfamily and play a critical role in cellular pace-making. Overall sequence conservation is high throughout the family, and channel functions are similar but not identical. Phylogenetic analyses are imperative to understand how these genes have evolved and to make informed comparisons of HCN structure and function. These have been previously limited, however, by the small number of available sequences, from a minimal number of species unevenly distributed over evolutionary time. We have now identified and annotated 31 novel genes from invertebrates, urochordates, fish, amphibians, birds, and mammals. With increased sequence numbers and a broader species representation, a more precise sequence comparison was performed and an evolutionary history for these genes was constructed. Our data confirm the existence of at least four vertebrate paralogs and suggest that these arose via three duplication and diversification events from a single ancestral gene. Additional lineage-specific duplications appear to have occurred in urochordate and fish genomes. Based on exon boundary conservation and phylogenetic analyses, we hypothesize that mammalian gene structure was established, and duplication events occurred, after the divergence of urochordates and before the divergence of fish from the tetrapod lineage. In addition, we identified highly conserved sequence regions that are likely important for general HCN functions, as well as regions with differences conserved among each of the individual paralogs. The latter may underlie more subtle isoform-specific properties that are otherwise masked by the high identity among mammalian orthologs and/or inaccurate alignments between paralogs.

scholarly journals Cladistic analysis of the family Stenothoidae (Amphipoda, Crustacea)

2006 ◽  
Vol 75 (03-04) ◽  
pp. 169-188 ◽  
Author(s):  
Traudl Krapp-Schickel ◽  
Stefan Koenemann
Keyword(s):  
Phylogenetic Analyses ◽  
Cladistic Analysis ◽  
Sensu Stricto ◽  
Individual Species ◽  
Family Status ◽  
The Family ◽  
The Individual

The amphipod family Stenothoidae contains more than 200 species in about 40 genera; these genera are at present often defined not by the presence, but by the absence of synapomorphies, thus defining grades rather than clades. Our phylogenetic analyses yielded 4 groups of stenothoids: a basic proboloidid clade; an advanced and always clearly separated Austral-Antarctic thaumatelsonid clade, with a possibly related Arctic mesometopid clade; and finally a poorly resolved group, the stenothoids sensu stricto, including the large and probably polyphyletic genera Stenothoe and Metopa, each with more than 50 species. It is proposed to study and analyse these groups separately in future, based on better redescriptions of the individual species. Our analyses support the family status of the Thaumatelsonidae, erected as a family by Gurjanova in 1938, but reduced to subfamily rank by Barnard in 1972.

scholarly journals Duplication and Diversification in the APETALA1/FRUITFULL Floral Homeotic Gene Lineage: Implications for the Evolution of Floral Development

Genetics ◽  
2003 ◽  
Vol 165 (2) ◽  
pp. 821-833 ◽  
Author(s):  
Amy Litt ◽  
Vivian F Irish
Keyword(s):  
Floral Development ◽  
Signal Sequence ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Mads Box ◽  
Mads Box Genes ◽  
C Terminus ◽  
Core Eudicots ◽  
Duplication Events ◽  
Angiosperm Species

Abstract Phylogenetic analyses of angiosperm MADS-box genes suggest that this gene family has undergone multiple duplication events followed by sequence divergence. To determine when such events have taken place and to understand the relationships of particular MADS-box gene lineages, we have identified APETALA1/FRUITFULL-like MADS-box genes from a variety of angiosperm species. Our phylogenetic analyses show two gene clades within the core eudicots, euAP1 (including Arabidopsis APETALA1 and Antirrhinum SQUAMOSA) and euFUL (including Arabidopsis FRUITFULL). Non-core eudicot species have only sequences similar to euFUL genes (FUL-like). The predicted protein products of euFUL and FUL-like genes share a conserved C-terminal motif. In contrast, predicted products of members of the euAP1 gene clade contain a different C terminus that includes an acidic transcription activation domain and a farnesylation signal. Sequence analyses indicate that the euAP1 amino acid motifs may have arisen via a translational frameshift from the euFUL/FUL-like motif. The euAP1 gene clade includes key regulators of floral development that have been implicated in the specification of perianth identity. However, the presence of euAP1 genes only in core eudicots suggests that there may have been changes in mechanisms of floral development that are correlated with the fixation of floral structure seen in this clade.

scholarly journals Klebsiella indica sp. nov., isolated from the surface of a tomato

2020 ◽  
Vol 70 (5) ◽  
pp. 3278-3286 ◽  
Author(s):  
Sukriti Gujarati ◽  
Diptaraj Chaudhari ◽  
Ashwini Hagir ◽  
Mitesh Khairnar ◽  
Yogesh Shouche ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Klebsiella Oxytoca ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Strain Nctc ◽  
Distinct Branch

A novel bacterial strain, designated TOUT106T, was isolated from the surface of a tomato. The cells were rod-shaped, Gram-negative, encapsulated and non-motile. Strain TOUT106T grows best at 28 °C and pH 7.0 and can tolerate up to 2 % (w/v) NaCl. Based on 16S rRNA gene phylogeny, strain TOUT106T was placed close to the Salmonella clade, with close similarity to Salmonella enterica subsp. arizonae strain NCTC 8297T (98.42 %). Results of genome-based phylogenetic analysis revealed that strain TOUT106T is placed well in the Klebsiella–Raoultella clade, by forming a distinct branch with Klebsiella michiganensis DSM25444T, Klebsiella oxytoca NCTC132727T, Klebsiella grimontii 06D021T and Klebsiella pasteurii SB6412T. The genomic DNA G+C content of strain TOUT106T is 53.53 mol%. The average nucleotide identity values of TOUT106T were less than 86.5 % with closely related members of the family Enterobacteriaceae . The major fatty acids of strain TOUT106T were C16 : 0, C17:0 cyclo, C14:0 3OH/C16:1 iso, C14 : 0, C19:0 cyclo ω8c, C18:1 ω6c/C18:1 ω7c, C12 : 0 and C16:1 ω7c/C16:1 ω6c. Strain TOUT106T showed differences in physiological, phenotypic and protein profiles by MALDI-TOF MS compared to its closest relatives. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain TOUT106T could be distinguished from the recognized species of the genus Klebsiella . It is suggested to represent a novel species of this genus, for which the name Klebsiella indica sp. nov. is proposed. The type strain is TOUT106T (=MCC 2901T=KACC 21384T=JCM 33718T).

scholarly journals Coexistence of Multiple Proteobacterial Endosymbionts in the Gills of the Wood-Boring Bivalve Lyrodus pedicellatus (Bivalvia: Teredinidae)

2002 ◽  
Vol 68 (12) ◽  
pp. 6292-6299 ◽  
Author(s):  
Daniel L. Distel ◽  
David J. Beaudoin ◽  
Wendy Morrill
Keyword(s):  
16S Rrna ◽  
Food Source ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Host Cells ◽  
Gram Negative Bacteria ◽  
The Family ◽  
In Situ Hybridizations ◽  
Wood Boring

ABSTRACT Wood-boring bivalves of the family Teredinidae (commonly called shipworms) are known to harbor dense populations of gram-negative bacteria within specialized cells (bacteriocytes) in their gills. These symbionts are thought to provide enzymes, e.g., cellulase and dinitrogenase, which assist the host in utilizing wood as a primary food source. A cellulolytic, dinitrogen-fixing bacterium, Teredinibacter turnerae, has been isolated from the gill tissues of numerous teredinid bivalves and has been proposed to constitute the sole or predominant symbiont of this bivalve family. Here we demonstrate that one teredinid species, Lyrodus pedicellatus, contains at least four distinct bacterial 16S rRNA types within its gill bacteriocytes, one of which is identical to that of T. turnerae. Phylogenetic analyses indicate that the three newly detected ribotypes are derived from gamma proteobacteria that are related to but distinct (>6.5% sequence divergence) from T. turnerae. In situ hybridizations with 16S rRNA-directed probes demonstrated that the pattern of occurrence of symbiont ribotypes within bacteriocytes was predictable and specific, with some bacteriocytes containing two symbiont ribotypes. However, only two of the six possible pairwise combinations of the four ribotypes were observed to cooccur within the same host cells. The results presented here are consistent with the existence of a complex multiple symbiosis in this shipworm species.

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