Amino acid δ 13 C and δ 15 N analyses reveal distinct species‐specific patterns of trophic plasticity in a marine symbiosis

Sequence Comparison of Vaginolysin from Different Gardnerella Species

Pathogens ◽

10.3390/pathogens10020086 ◽

2021 ◽

Vol 10 (2) ◽

pp. 86

Author(s):

Erin M. Garcia ◽

Myrna G. Serrano ◽

Laahirie Edupuganti ◽

David J. Edwards ◽

Gregory A. Buck ◽

...

Keyword(s):

Amino Acid ◽

Human Microbiome ◽

Human Microbiome Project ◽

Distinct Species ◽

Vaginal Swab ◽

Metagenomic Data ◽

Gardnerella Vaginalis ◽

Vaginal Epithelial Cells ◽

Species Specific

Gardnerella vaginalis has recently been split into 13 distinct species. In this study, we tested the hypotheses that species-specific variations in the vaginolysin (VLY) amino acid sequence could influence the interaction between the toxin and vaginal epithelial cells and that VLY variation may be one factor that distinguishes less virulent or commensal strains from more virulent strains. This was assessed by bioinformatic analyses of publicly available Gardnerella spp. sequences and quantification of cytotoxicity and cytokine production from purified, recombinantly produced versions of VLY. After identifying conserved differences that could distinguish distinct VLY types, we analyzed metagenomic data from a cohort of female subjects from the Vaginal Human Microbiome Project to investigate whether these different VLY types exhibited any significant associations with symptoms or Gardnerella spp.-relative abundance in vaginal swab samples. While Type 1 VLY was most prevalent among the subjects and may be associated with increased reports of symptoms, subjects with Type 2 VLY dominant profiles exhibited increased relative Gardnerella spp. abundance. Our findings suggest that amino acid differences alter the interaction of VLY with vaginal keratinocytes, which may potentiate differences in bacterial vaginosis (BV) immunopathology in vivo.

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Codon harmonization reduces amino acid misincorporation in bacterially expressed P. falciparum proteins and improves their immunogenicity

AMB Express ◽

10.1186/s13568-019-0890-6 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Neeraja Punde ◽

Jennifer Kooken ◽

Dagmar Leary ◽

Patricia M. Legler ◽

Evelina Angov

Keyword(s):

Protein Structure ◽

Amino Acid ◽

Codon Usage ◽

Dna Sequences ◽

Structural Integrity ◽

Host Cells ◽

Loss Of Function ◽

Species Specific ◽

And Function ◽

The Impact

Abstract Codon usage frequency influences protein structure and function. The frequency with which codons are used potentially impacts primary, secondary and tertiary protein structure. Poor expression, loss of function, insolubility, or truncation can result from species-specific differences in codon usage. “Codon harmonization” more closely aligns native codon usage frequencies with those of the expression host particularly within putative inter-domain segments where slower rates of translation may play a role in protein folding. Heterologous expression of Plasmodium falciparum genes in Escherichia coli has been a challenge due to their AT-rich codon bias and the highly repetitive DNA sequences. Here, codon harmonization was applied to the malarial antigen, CelTOS (Cell-traversal protein for ookinetes and sporozoites). CelTOS is a highly conserved P. falciparum protein involved in cellular traversal through mosquito and vertebrate host cells. It reversibly refolds after thermal denaturation making it a desirable malarial vaccine candidate. Protein expressed in E. coli from a codon harmonized sequence of P. falciparum CelTOS (CH-PfCelTOS) was compared with protein expressed from the native codon sequence (N-PfCelTOS) to assess the impact of codon usage on protein expression levels, solubility, yield, stability, structural integrity, recognition with CelTOS-specific mAbs and immunogenicity in mice. While the translated proteins were expected to be identical, the translated products produced from the codon-harmonized sequence differed in helical content and showed a smaller distribution of polypeptides in mass spectra indicating lower heterogeneity of the codon harmonized version and fewer amino acid misincorporations. Substitutions of hydrophobic-to-hydrophobic amino acid were observed more commonly than any other. CH-PfCelTOS induced significantly higher antibody levels compared with N-PfCelTOS; however, no significant differences in either IFN-γ or IL-4 cellular responses were detected between the two antigens.

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Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C

10.7287/peerj.preprints.3153v2 ◽

2017 ◽

Author(s):

Maria A Prostova ◽

Andrei A Deviatkin ◽

Irina O Tcelykh ◽

Alexander N Lukashev ◽

Anatoly P Gmyl

Keyword(s):

Amino Acid ◽

Genome Stability ◽

Rna Binding ◽

Apical Region ◽

Reading Frame ◽

Loop Region ◽

Binding Partners ◽

D Loop ◽

The One ◽

Species Specific

Background. Enteroviruses are small non-enveloped viruses with (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features low fidelity, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein. Methods.To evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C. Results.A total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y=U/C, N=any nucleotide, H=A/C/U). The putative RNA-binding tripeptide 154-156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific. Discussion. Despite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition.

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Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C

10.7287/peerj.preprints.3153 ◽

2017 ◽

Author(s):

Maria A Prostova ◽

Andrei A Deviatkin ◽

Irina O Tcelykh ◽

Alexander N Lukashev ◽

Anatoly P Gmyl

Keyword(s):

Amino Acid ◽

Genome Stability ◽

Rna Binding ◽

Apical Region ◽

Reading Frame ◽

Loop Region ◽

Binding Partners ◽

D Loop ◽

The One ◽

Species Specific

Background. Enteroviruses are small non-enveloped viruses with (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features low fidelity, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein. Methods.To evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C. Results.A total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y=U/C, N=any nucleotide, H=A/C/U). The putative RNA-binding tripeptide 154-156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific. Discussion. Despite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition.

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Microbiomes of pathogenic Vibrio species reveal environmental and planktonic associations

10.21203/rs.2.18876/v1 ◽

2019 ◽

Author(s):

Rachel E. Diner ◽

Ariel J. Rabines ◽

Hong Zheng ◽

Joshua A. Steele ◽

John F. Griffith ◽

...

Keyword(s):

Distinct Species ◽

Human Infection ◽

Model Systems ◽

Taxonomic Resolution ◽

Environmental Preferences ◽

Pathogenic Vibrio ◽

Photosynthetic Organism ◽

One Year ◽

Species Specific ◽

Planktonic Community

Abstract Background Many species of coastal Vibrio spp. bacteria can infect humans, representing an emerging health threat linked to increasing seawater temperatures. Vibrio interactions with the planktonic community impact coastal ecology and human infection potential. In particular, interactions with eukaryotic and photosynthetic organism may provide attachment substrate and critical nutrients (e.g. chitin, phytoplankton exudates) that facilitate the persistence, diversification, and spread of pathogenic Vibrio spp. Vibrio interactions with these organisms in an environmental context are, however, poorly understood.Results We quantified pathogenic Vibrio species, including V. cholerae, V. parahaemolyticus, and V. vulnificus, and two virulence-associated genes for one year at five coastal sites in Southern California and used metabarcoding to profile associated prokaryotic and eukaryotic communities, including vibrio-specific communities. These Vibrio spp. reached high abundances, particularly during Summer months, and inhabited distinct species-specific environmental niches driven by temperature and salinity. Associated bacterial and eukaryotic taxa identified at fine-scale taxonomic resolution revealed genus and species-level relationships. For example, common Thalassiosira genera diatoms capable of exuding chitin were positively associated with V. cholerae and V. vulnificus in a species-specific manner, while the most abundant eukaryotic genus, the diatom Chaetoceros, was positively associated with V. parahaemolyticus. Associations were often linked to shared environmental preferences, and several copepod genera were linked to low-salinity environmental conditions and abundant V. cholerae and V. vulnificus.Conclusions This study clarifies ecological relationships between pathogenic Vibrio spp. and the planktonic community, elucidating new functionally relevant associations, establishing a workflow for examining environmental pathogen microbiomes, and highlighting prospective model systems for future mechanistic studies.

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Amino acid sequence variations in Nicotiana CRR4 orthologs determine the species-specific efficiency of RNA editing in plastids

Nucleic Acids Research ◽

10.1093/nar/gkn629 ◽

2008 ◽

Vol 36 (19) ◽

pp. 6155-6164 ◽

Cited By ~ 23

Author(s):

Kenji Okuda ◽

Yuya Habata ◽

Yoshichika Kobayashi ◽

Toshiharu Shikanai

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Rna Editing ◽

Sequence Variations ◽

Species Specific

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Genetic, morphometric, and molecular analyses of interspecies differences in head shape and hybrid developmental defects in the wasp genus Nasonia

10.1101/663732 ◽

2019 ◽

Cited By ~ 2

Author(s):

Lorna B Cohen ◽

Rachel Edwards ◽

Dyese Moody ◽

Deanna Arsala ◽

Jack H Werren ◽

...

Keyword(s):

Parasitoid Wasp ◽

Gene Interaction ◽

Distinct Species ◽

Diploid Male ◽

Gene Interactions ◽

Morphological Development ◽

Head Shape ◽

Developmental Defects ◽

Primary Driver ◽

Species Specific

AbstractMales in the parasitoid wasp genus Nasonia (N. vitripennis, N. giraulti, N. longicornis) have distinct, species specific, head shapes. Fertile hybrids among the species are readily produced in the lab allowing genetic analysis of the evolved differences. In addition, the obligate haploidy of males makes these wasps a uniquely powerful model for analyzing the role of complex gene interactions in development and evolution. Previous analyses have shown that complex gene interactions underpin different aspects of the shape differences, and developmental incompatibilities that are specific to the head in F2 haploid hybrid males are also governed by networks of gene interaction. Here we use the genetic tools available in Nasonia to extend our understanding of the gene interactions that affect development and morphogenesis in male heads. Using artificial diploid male hybrids, we show that alleles affecting head shape are codominant, leading to uniform, averaged hybrid F1 diploid male heads, while the alleles mediating developmental defects are recessive, and are not visible in the diploid hybrids. We also determine that divergence in time, rather than in morphological disparity is the primary driver of hybrid developmental defects. In addition, we show that doublesex is necessary for the male head shape differences, but is not the only important factor. Finally we demonstrate that we can dissect complex interspecies gene interaction networks using introgression in this system. These advances represent significant progress in the complex web of gene interactions that govern morphological development, and chart the connections between genomic and phenotypic variation.

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31P-NMR Metabolomics Revealed Species-Specific Use of Phosphorous in Trees of a French Guiana Rainforest

Molecules ◽

10.3390/molecules25173960 ◽

2020 ◽

Vol 25 (17) ◽

pp. 3960

Author(s):

Albert Gargallo-Garriga ◽

Jordi Sardans ◽

Joan Llusià ◽

Guille Peguero ◽

Dolores Asensio ◽

...

Keyword(s):

Tree Species ◽

French Guiana ◽

31P Nmr ◽

Principal Component ◽

Distinct Species ◽

Community Diversity ◽

N:P Ratios ◽

High Concentrations ◽

Species Specific ◽

Total P

Productivity of tropical lowland moist forests is often limited by availability and functional allocation of phosphorus (P) that drives competition among tree species and becomes a key factor in determining forestall community diversity. We used non-target 31P-NMR metabolic profiling to study the foliar P-metabolism of trees of a French Guiana rainforest. The objective was to test the hypotheses that P-use is species-specific, and that species diversity relates to species P-use and concentrations of P-containing compounds, including inorganic phosphates, orthophosphate monoesters and diesters, phosphonates and organic polyphosphates. We found that tree species explained the 59% of variance in 31P-NMR metabolite profiling of leaves. A principal component analysis showed that tree species were separated along PC 1 and PC 2 of detected P-containing compounds, which represented a continuum going from high concentrations of metabolites related to non-active P and P-storage, low total P concentrations and high N:P ratios, to high concentrations of P-containing metabolites related to energy and anabolic metabolism, high total P concentrations and low N:P ratios. These results highlight the species-specific use of P and the existence of species-specific P-use niches that are driven by the distinct species-specific position in a continuum in the P-allocation from P-storage compounds to P-containing molecules related to energy and anabolic metabolism.

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The Anopheles maculipennis complex (Diptera: Culicidae) in Iran: molecular characterization and recognition of a new species

Bulletin of Entomological Research ◽

10.1079/ber2003272 ◽

2003 ◽

Vol 93 (6) ◽

pp. 527-535 ◽

Cited By ~ 49

Author(s):

M.M. Sedaghat ◽

Y.-M. Linton ◽

M.A. Oshaghi ◽

H. Vatandoost ◽

R.E. Harbach

Keyword(s):

New Species ◽

Distinct Species ◽

Nuclear Rdna ◽

Pcr Assay ◽

Dna Evidence ◽

Anopheles Maculipennis Complex ◽

Anopheles Maculipennis ◽

Species Specific ◽

A New Species ◽

Maculipennis Complex

AbstractMosquitoes of the Anopheles maculipennis complex were collected in nine provinces of Iran (Esfahan, Fars, Gilan, Golestan, Kohkiluyeh va Boyerahmad, Mazandaran, Tehran, Azarbaijan-e Gharbi and Zanjan) between June 1983 and September 2002. The nuclear rDNA ITS2 sequences of 86 specimens were compared with those of seven species of the complex available in GenBank. Three genetically distinct species of the complex were distinguished: A. maculipennis Meigen, A. sacharovi Favre and a previously unrecognized species. The last species is most similar to, but clearly distinct from, A. martinius Shingarev and A. sacharovi. The taxonomy of A. martinius and A. sacharovi is critically reviewed, and justification is provided for formally recognizing the third species as Anopheles persiensissp.n. The new species is the first culicid to be characterized and named principally on the basis of DNA evidence. Anopheles persiensis was collected only in the northern Caspian Sea littoral provinces of Gilan and Mazandaran, and it seems likely that this species could be responsible for malaria transmission in this region that was previously attributed to A. maculipennis. A species-specific RFLP–PCR assay based on ITS2 sequences was developed to facilitate further studies of the three species in Iran.

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Molecular cloning and evolutionary analysis of the GJA1 (connexin43) gene from bats (Chiroptera)

Genetics Research ◽

10.1017/s0016672309000032 ◽

2009 ◽

Vol 91 (2) ◽

pp. 101-109 ◽

Cited By ~ 1

Author(s):

LI WANG ◽

GANG LI ◽

JINHONG WANG ◽

SHAOHUI YE ◽

GARETH JONES ◽

...

Keyword(s):

Amino Acid ◽

Phylogenetic Reconstruction ◽

Purifying Selection ◽

Likelihood Method ◽

Evolutionary Analysis ◽

Coding Region ◽

Specific Amino Acid ◽

Junction Protein ◽

Gap Junction Protein ◽

Species Specific

SummaryGap junction protein connexin43 (Cx43), encoded by the GJA1 gene, is the most abundant connexin in the cardiovascular system and was reported as a crucial factor maintaining cardiac electrical conduction, as well as having a very important function in facilitating the recycling of potassium ions from hair cells in the cochlea back into the cochlear endolymph during auditory transduction processes. In mammals, bats are the only taxon possessing powered flight, placing exceptional demand on many organismal processes. To meet the demands of flying, the hearts of bats show many specialties. Moreover, ultrasonic echolocation allows bat species to orientate and often detect and locate food in darkness. In this study, we cloned the full-length coding region of GJA1 gene from 12 different species of bats and obtained orthologous sequences from other mammals. We used the maximum likelihood method to analyse the evolution of GJA1 gene in mammals and the lineage of bats. Our results showed this gene is much conserved in mammals, as well as in bats' lineage. Compared with other mammals, we found one private amino acid substitution shared by bats, which is located on the inner loop domain, as well as some species-specific amino acid substitutions. The evolution rate analyses showed the signature of purifying selection on not only different classification level lineages but also the different domains and amino acid residue sites of this gene. Also, we suggested that GJA1 gene could be used as a good molecular marker to do the phylogenetic reconstruction.

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