Structure, expression and phylogenetic analysis of the gene encoding actin I in Pneumocystis carinii.

Abstract Actin is a major component of the cytoskeleton and one of the most abundant proteins found in eukaryotic cells. Comparative sequence analysis shows that this essential gene has been highly conserved throughout eukaryotic evolution making it useful for phylogenetic analysis. Complete cDNA clones for the actin-encoding gene were isolated and characterized from Pneumocystis carinii purified from immunosuppressed rat lungs. The nucleotide sequence encodes a protein of 376 amino acids. The predicted actin protein of P. carinii shares a high degree of conservation to other known actins. Only one major actin gene was found in P. carinii. The P. carinii actin sequence was compared with 30 other actin sequences. Gene phylogenies constructed using both neighbor-joining and protein parsimony methods places the P. carinii actin sequence closest to the majority of the fungi. Since the phylogenetic relationship of P. carinii to fungi and protists has been questioned, these data on the actin gene phylogeny support the grouping of P. carinii with the fungi.

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Essential and nonessential histone H2A variants in Tetrahymena thermophila.

Molecular and Cellular Biology ◽

10.1128/mcb.16.8.4305 ◽

1996 ◽

Vol 16 (8) ◽

pp. 4305-4311 ◽

Cited By ~ 81

Author(s):

X Liu ◽

B Li ◽

GorovskyMA

Keyword(s):

Tetrahymena Thermophila ◽

Essential Gene ◽

Histone Variants ◽

Gene Replacement ◽

Histone H2a ◽

Gene Encoding ◽

Genes Encoding ◽

Simple Mass ◽

Essential Function ◽

High Degree

Although variants have been identified for every class of histone, their functions remain unknown. We have been studying the histone H2A variant hv1 in the ciliated protozoan Tetrahymena thermophila. Sequence analysis indicates that hv1 belongs to the H2A.F/Z type of histone variants. On the basis of the high degree of evolutionary conservation of this class of histones, they are proposed to have one or more distinct and essential functions that cannot be performed by their major H2A counterparts. Considerable evidence supports the hypothesis that the hv1 protein in T. thermophila and hv1-like proteins in other eukaryotes are associated with active chromatin. In T. thermophila, simple mass transformation and gene replacement techniques have recently become available. In this report, we demonstrate that either the HTA1 gene or the HTA2 gene, encoding the major H2As, can be completely replaced by disrupted genes in the polyploid, transcriptionally active macronucleus, indicating that neither of the two genes is essential. However, only some of the HTA3 genes encoding hv1 can be replaced by disrupted genes, indicating that the H2A.F/Z type variants have an essential function that cannot be performed by the major H2A genes. Thus, an essential gene in T. thermophila can be defined by the fact that it can be partially, but not completely, eliminated from the polyploid macronucleus. To our knowledge, this study represents the first use of gene disruption technology to study core histone gene function in any organism other than yeast and the first demonstration of an essential gene in T. thermophila using these methods. When a rescuing plasmid carrying a wild-type HTA3 gene was introduced into the T. thermophila cells, the endogenous chromosomal HTA3 could be completely replaced, defining a gene replacement strategy that can be used to analyze the function of essential genes.

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Sequencing, Cloning, and High-Level Expression of the pfp Gene, Encoding a PPi-Dependent Phosphofructokinase from the Extremely Thermophilic EubacteriumDictyoglomus thermophilum

Journal of Bacteriology ◽

10.1128/jb.182.16.4661-4666.2000 ◽

2000 ◽

Vol 182 (16) ◽

pp. 4661-4666 ◽

Cited By ~ 12

Author(s):

Yan-Huai R. Ding ◽

Ron S. Ronimus ◽

Hugh W. Morgan

Keyword(s):

Phylogenetic Analysis ◽

Cloning And Expression ◽

High Level Expression ◽

Gene Encoding ◽

Thermoproteus Tenax ◽

High Level ◽

High Degree ◽

Dictyoglomus Thermophilum ◽

Degree Of Similarity

ABSTRACT The sequencing, cloning, and expression of the pfp gene from Dictyoglomus thermophilum, which consists of 1,041 bp and encodes a pyrophosphate-dependent phosphofructokinase, are described. A phylogenetic analysis indicates that the enzyme is closely related to the pyrophosphate-dependent enzyme from Thermoproteus tenax. The recombinant and native enzymes share a high degree of similarity for most properties examined.

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Phylogenetic Characterization of the Palyam Serogroup Orbiviruses

Viruses ◽

10.3390/v11050446 ◽

2019 ◽

Vol 11 (5) ◽

pp. 446 ◽

Cited By ~ 3

Author(s):

Karen Ebersohn ◽

Peter Coetzee ◽

Louwrens P. Snyman ◽

Robert Swanepoel ◽

Estelle H. Venter

Keyword(s):

Phylogenetic Analysis ◽

Sequence Data ◽

Evolutionary Relationship ◽

Full Genome Sequence ◽

African Horse Sickness Virus ◽

Gene Encoding ◽

Phylogenetic Characterization ◽

Next Generation Sequencing Ngs ◽

High Degree

The Palyam serogroup orbiviruses are associated with abortion and teratogenesis in cattle and other ruminants. Of the 13 different serotypes that have been identified, the full genome sequence of only one, Kasba, has been published. We undertook to perform Next Generation Sequencing (NGS) and phylogenetic analysis on 12 Palyam serotypes plus field isolates of the African serotypes in our possession. The Palyam serogroup was found to be most closely related to the African horse sickness virus group and showed the most distant evolutionary relationship to the equine encephalosis viruses (EEV). Amino acid sequence analysis revealed that the gene encoding VP7 was the most conserved within serotypes and VP2 and VP5 showed the highest degree of variation. A high degree of sequence identity was found for isolates from the same geographical region. The phylogenetic analysis revealed two clades where the African serotypes were all very closely related in one clade and the other clade contained the Australian and Asian serotypes and one African serotype, Petevo. It was evident from the sequence data that the geographical origin of Palyam serogroup viruses played an important role in the development of the different serotypes.

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EVOLUTION AND VARIATION OF RENIN GENES IN MICE

Genetics ◽

10.1093/genetics/108.3.651 ◽

1984 ◽

Vol 108 (3) ◽

pp. 651-667

Author(s):

Douglas P Dickinson ◽

Kenneth W Gross ◽

Nina Piccini ◽

Carol M Wilson

Keyword(s):

Gene Expression ◽

Submandibular Gland ◽

Regulation Of Gene Expression ◽

Inbred Strains ◽

Duplication Event ◽

Comparative Sequence Analysis ◽

Chromosome 1 ◽

Gene Encoding ◽

Prior Estimate ◽

Low Levels

ABSTRACT Inbred strains of mice carry Ren-1, a gene encoding the thermostable Renin-1 isozyme. Ren-1 is expressed at relatively low levels in mouse submandibular gland and kidney. Some strains also carry Ren-2, a gene encoding the thermolabile Renin-2 isozyme. Ren-2 is expressed at high levels in the mouse submandibular gland and at very low levels, if at all, in the kidney. Ren-1 and Ren-2 are closely linked on mouse chromosome 1, show extensive homology in coding and noncoding regions and provide a model for studying the regulation of gene expression. An investigation of renin genes and enzymatic activity in wild-derived mice identified several restriction site polymorphisms as well as putative variants in renin gene expression and protein structure. The number of renin genes carried by different subpopulations of wild-derived mice is consistent with the occurrence of a gene duplication event prior to the divergence of M. spretus (2.75-5.5 million yr ago). This conclusion is in agreement with a prior estimate based upon comparative sequence analysis of Ren-1 and Ren-2 from inbred laboratory mice.

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Gene Sequencing and Phylogenetic Analysis: Powerful Tools for an Improved Diagnosis of Fish Mycobacteriosis Caused by Mycobacterium fortuitum Group Members

Microorganisms ◽

10.3390/microorganisms9040797 ◽

2021 ◽

Vol 9 (4) ◽

pp. 797

Author(s):

Davide Mugetti ◽

Mattia Tomasoni ◽

Paolo Pastorino ◽

Giuseppe Esposito ◽

Vasco Menconi ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Gene Sequencing ◽

Diagnostic Techniques ◽

Individual Species ◽

Identification System ◽

Mycobacterium Fortuitum ◽

Biochemical Tests ◽

Species Determination ◽

Gene Encoding ◽

The Individual

The Mycobacterium fortuitum group (MFG) consists of about 15 species of fast-growing nontuberculous mycobacteria (NTM). These globally distributed microorganisms can cause diseases in humans and animals, especially fish. The increase in the number of species belonging to MFG and the diagnostic techniques panel do not allow to clarify their real clinical significance. In this study, biomolecular techniques were adopted for species determination of 130 isolates derived from fish initially identified through biochemical tests as NTM belonging to MFG. Specifically, gene sequencing and phylogenetic analysis were used based on a fragment of the gene encoding the 65 KDa heat shock protein (hsp65). The analyzes made it possible to confirm that all the isolates belong to MFG, allowing to identify the strains at species level. Phylogenetic analysis substantially confirmed what was obtained by gene sequencing, except for six strains; this is probably due to the sequences present in NCBI database. Although the methodology used cannot represent a univocal identification system, this study has allowed us to evaluate its effectiveness as regards the species of MFG. Future studies will be necessary to apply these methods with other gene fragments and to clarify the real pathogenic significance of the individual species of this group of microorganisms.

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The Novel ALG-2 Target Protein CDIP1 Promotes Cell Death by Interacting with ESCRT-I and VAPA/B

International Journal of Molecular Sciences ◽

10.3390/ijms22031175 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1175

Author(s):

Ryuta Inukai ◽

Kanako Mori ◽

Keiko Kuwata ◽

Chihiro Suzuki ◽

Masatoshi Maki ◽

...

Keyword(s):

Cell Death ◽

Essential Gene ◽

Susceptibility Gene ◽

Target Protein ◽

Hek293 Cells ◽

Dependent Manner ◽

Gene Encoding ◽

Endosomal Sorting ◽

Cell Death Pathways ◽

Apoptotic Protein

Apoptosis-linked gene 2 (ALG-2, also known as PDCD6) is a member of the penta-EF-hand (PEF) family of Ca2+-binding proteins. The murine gene encoding ALG-2 was originally reported to be an essential gene for apoptosis. However, the role of ALG-2 in cell death pathways has remained elusive. In the present study, we found that cell death-inducing p53 target protein 1 (CDIP1), a pro-apoptotic protein, interacts with ALG-2 in a Ca2+-dependent manner. Co-immunoprecipitation analysis of GFP-fused CDIP1 (GFP-CDIP1) revealed that GFP-CDIP1 associates with tumor susceptibility gene 101 (TSG101), a known target of ALG-2 and a subunit of endosomal sorting complex required for transport-I (ESCRT-I). ESCRT-I is a heterotetrameric complex composed of TSG101, VPS28, VPS37 and MVB12/UBAP1. Of diverse ESCRT-I species originating from four VPS37 isoforms (A, B, C, and D), CDIP1 preferentially associates with ESCRT-I containing VPS37B or VPS37C in part through the adaptor function of ALG-2. Overexpression of GFP-CDIP1 in HEK293 cells caused caspase-3/7-mediated cell death. In addition, the cell death was enhanced by co-expression of ALG-2 and ESCRT-I, indicating that ALG-2 likely promotes CDIP1-induced cell death by promoting the association between CDIP1 and ESCRT-I. We also found that CDIP1 binds to vesicle-associated membrane protein-associated protein (VAP)A and VAPB through the two phenylalanines in an acidic tract (FFAT)-like motif in the C-terminal region of CDIP1, mutations of which resulted in reduction of CDIP1-induced cell death. Therefore, our findings suggest that different expression levels of ALG-2, ESCRT-I subunits, VAPA and VAPB may have an impact on sensitivity of anticancer drugs associated with CDIP1 expression.

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Phylogenetic Analysis of Perkinsus Based on Actin Gene Sequences

Journal of Parasitology ◽

10.2307/3284403 ◽

1997 ◽

Vol 83 (3) ◽

pp. 417 ◽

Cited By ~ 61

Author(s):

Kimberly S. Reece ◽

Mark E. Siddall ◽

Eugene M. Burreson ◽

John E. Graves

Keyword(s):

Phylogenetic Analysis ◽

Actin Gene ◽

Gene Sequences

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Structure and expression of human IgG FcRII(CD32). Functional heterogeneity is encoded by the alternatively spliced products of multiple genes.

Journal of Experimental Medicine ◽

10.1084/jem.170.4.1369 ◽

1989 ◽

Vol 170 (4) ◽

pp. 1369-1385 ◽

Cited By ~ 200

Author(s):

D G Brooks ◽

W Q Qiu ◽

A D Luster ◽

J V Ravetch

Keyword(s):

Structural Heterogeneity ◽

Amino Acid Sequences ◽

Cdna Clones ◽

Membrane Glycoproteins ◽

Igg Binding ◽

Genes Expression ◽

Alternatively Spliced ◽

Membrane Spanning ◽

High Degree ◽

Membrane Spanning Domains

The structural heterogeneity of the human low affinity receptor for IgG, FcRII(CD32), has been elucidated through the isolation, characterization, and expression of cDNA clones derived from myeloid and lymphoid RNA. These clones predict amino acid sequences consistent with integral membrane glycoproteins with single membrane spanning domains. The extracellular domains display sequence homology to other Fc gamma Rs and members of the Ig supergene family. A minimum of three genes (Fc gamma RIIa, IIa', and Fc gamma RIIb) encode these transcripts, which demonstrate highly related extracellular and membrane spanning domains. IIa/IIa' differ substantially in the intracytoplasmic domain from IIb. Alternative splicing of the IIb gene generates further heterogeneity in both NH2- and COOH-terminal domains of the predicted proteins. Comparison to the murine homologues of these molecules reveals a high degree of conservation between the products of one of these genes, Fc gamma RIIb, and the murine beta gene in primary sequence, splicing pattern, and tissue distribution. In contrast, the sequence of IIa' indicates its relationship to the beta-like genes, with mutation giving rise to a novel cytoplasmic domain, while IIa is a chimera of both alpha- and beta-like genes. Expression of these cDNA molecules by transfection results in the appearance of IgG binding molecules that bear the epitopes defined by the FcRII(CD32) mAbs previously described.

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Interactions Between Chill-Hours and Degree-Days Affect Carpogenic Germination in Monilinia vaccinii-corymbosi

Phytopathology ◽

10.1094/phyto.2001.91.1.77 ◽

2001 ◽

Vol 91 (1) ◽

pp. 77-83 ◽

Cited By ~ 22

Author(s):

H. Scherm ◽

A. T. Savelle ◽

P. L. Pusey

Keyword(s):

Laboratory Experiments ◽

Field Experiments ◽

Degree Days ◽

Carpogenic Germination ◽

Conditioning Period ◽

Low Degree ◽

Heating Degree Days ◽

Relationship Of ◽

High Degree ◽

The Relationship

The relationship of cumulative chill-hours (hours with a mean temperature <7.2°C) and heating degree-days (base 7.2°C) to carpogenic germination of pseudosclerotia of Monilinia vaccinii-corymbosi, which causes mummy berry disease of blueberry, was investigated. In two laboratory experiments, pseudosclerotia collected from rabbiteye blueberry in Georgia were conditioned at 5 to 6°C for 26 to 1,378 h prior to placement in conditions favorable for germination and apothecium development. The number of chill-hours accumulated during the conditioning period affected the subsequent proportion of pseudosclerotia that germinated and produced apothecia, with the greatest incidence of carpogenic germination occurring after intermediate levels of chilling (≈700 chill-hours). The minimum chilling requirement for germination and apothecium production was considerably lower than that reported previously for pseudo-sclerotia from highbush blueberry in northern production regions. The rate of carpogenic germination was strongly affected by interactions between the accumulation of chill-hours and degree-days during the conditioning and germination periods; pseudosclerotia exposed to prolonged chilling periods, once transferred to suitable conditions, germinated and produced apothecia more rapidly (after fewer degree-days had accumulated) than those exposed to shorter chilling periods. Thus, pseudosclerotia of M. vaccinii-corymbosi are adapted to germinate carpogenically following cold winters (high chill-hours, low degree-days) as well as warm winters (low chill-hours, high degree-days). Results were validated in a combined field-laboratory experiment in which pseudosclerotia that had received various levels of natural chilling were allowed to germinate in controlled conditions in the laboratory, and in two field experiments in which pseudosclerotia were exposed to natural chilling and germination conditions. A simple model describing the timing of apothecium emergence in relation to cumulative chill-hours and degree-days was developed based on the experiments. The model should be useful for better timing of field scouting programs for apothecia to aid in management of primary infection by M. vaccinii-corymbosi.

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Novel chicken actin gene: third cytoplasmic isoform

Molecular and Cellular Biology ◽

10.1128/mcb.5.5.1151-1162.1985 ◽

1985 ◽

Vol 5 (5) ◽

pp. 1151-1162

Author(s):

D J Bergsma ◽

K S Chang ◽

R J Schwartz

Keyword(s):

Nucleotide Sequence ◽

Single Copy ◽

Actin Gene ◽

Single Copy Gene ◽

Gene Diversification ◽

Mrna Transcripts ◽

Copy Gene ◽

Actin Mrna ◽

Distinct Member ◽

Actin Protein

We identified a novel chicken actin gene. The actin protein deduced from its nucleotide sequence very closely resembles the vertebrate cytoplasmic actins; accordingly, we classified this gene as a nonmuscle type. We adopted the convention for indicating the nonmuscle actins of the class Amphibia (Vandekerckhove et al., J. Mol. Biol. 152:413-426) and denoted this gene as type 5. RNA blot analysis demonstrated that the type 5 actin mRNA transcripts accumulate in adult tissues in a pattern indicative of a nonmuscle actin gene. Genomic DNA blots indicated that the type 5 actin is a single copy gene and a distinct member of the chicken actin multigene family. Inspection of the nucleotide sequence revealed many features that distinguished the type 5 gene from all other vertebrate actin genes examined to date. These unique characteristics include: (i) an initiation Met codon preceding an Ala codon, a feature previously known only in plant actins, (ii) a single intron within the 5' untranslated region, with no interruptions in the coding portion of the gene, and (iii) an atypical Goldberg-Hogness box (ATAGAA) preceding the mRNA initiation terminus. These unusual features have interesting implications for actin gene diversification during evolution.

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