scholarly journals A Carbohydrate Hydrolysis Enzymes encoding Genes in Neurospora crassa

2015 ◽  
Vol 5 (3) ◽  
pp. 711-727
Author(s):  
Ravi Gedela
Keyword(s):  
Neurospora Crassa ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
High Sequence Similarity ◽  
Physiochemical Properties ◽  
Carbohydrate Hydrolysis ◽  
Genes Encoding ◽  
Multiple Sequences ◽  
Encoding Genes ◽  
Sequences Alignment

Neurospora crassa, NCU05882.7 (423aa) and NCU09774.7 (303 aa) (NCU, Neurospora 7 crassa unit) genes encoding a Cellulase, which hydrolysis the Cellulose. In addition to that, 8 reporting here other 35 Carbohydrate hydrolysis enzymes encoding genes in N.crassa. A 9 metagenomic analysis for multiple sequences alignment and Phylogenetics analysis, the evaluated 10 result showed high sequence similarity and 99% homology to the other class of fungi; in the 11 bacterial species showed extremely very less sequence similarities and 100 % homology. 12 Where as in inter species between fungi and bacteria, the results showed extremely less sequence 13 similarities and 97 % homology. The studies on physiochemical properties of Cellulase using 14 GeneDoc, the evaluated results showed Cellulase was an amphoteric (polor), aromatic, aliphatic 15 and highly repeated amino acids of glycine and proline. These metagenomic studies could help 16 to straightforward isolation of Cellulase enzymes from NCU05882.7 (Chromosome/Linkage 17 Group-VII), NCU09774.7 (Chromosome Linkage Group- II) and other 35 Carbohydrate 18 hydrolysis enzymes encoding genes in N.crassa.

scholarly journals Evolution of Chi motifs in Proteobacteria

2021 ◽  
Author(s):  
Angélique Buton ◽  
Louis-Marie Bobay
Keyword(s):  
Sequence Similarity ◽  
Bacterial Species ◽  
Double Strand Breaks ◽  
Dna Double Strand Breaks ◽  
Large Dataset ◽  
High Sequence Similarity ◽  
Strand Breaks ◽  
E Coli ◽  
Dna Motif ◽  
And Staphylococcus Aureus

Abstract Homologous recombination is a key pathway found in nearly all bacterial taxa. The recombination complex allows bacteria to repair DNA double strand breaks but also promotes adaption through the exchange of DNA between cells. In Proteobacteria, this process is mediated by the RecBCD complex, which relies on the recognition of a DNA motif named Chi to initiate recombination. The Chi motif has been characterized in Escherichia coli and analogous sequences have been found in several other species from diverse families, suggesting that this mode of action is widespread across bacteria. However, the sequences of Chi-like motifs are known for only five bacterial species: E. coli, Haemophilus influenzae, Bacillus subtilis, Lactococcus lactis and Staphylococcus aureus. In this study we detected putative Chi motifs in a large dataset of Proteobacteria and we identified four additional motifs sharing high sequence similarity and similar properties to the Chi motif of E. coli in 85 species of Proteobacteria. Most Chi motifs were detected in Enterobacteriaceae and this motif appears well conserved in this family. However, we did not detect Chi motifs for the majority of Proteobacteria, suggesting that different motifs are used in these species. Altogether these results substantially expand our knowledge on the evolution of Chi motifs and on the recombination process in bacteria.

scholarly journals Transgene-Induced Silencing of the Zoosporogenesis-Specific NIFC Gene Cluster of Phytophthora infestans Involves Chromatin Alterations

2007 ◽  
Vol 6 (7) ◽  
pp. 1200-1209 ◽  
Author(s):  
Howard S. Judelson ◽  
Shuji Tani
Keyword(s):  
Phytophthora Infestans ◽  
Gene Cluster ◽  
Sequence Similarity ◽  
Transcriptional Regulator ◽  
Hairpin Rna ◽  
High Sequence Similarity ◽  
Genes Encoding ◽  
Cognate Gene ◽  
Chromatin Packing ◽  
Nif Proteins

ABSTRACT Clustered within the genome of the oomycete phytopathogen Phytophthora infestans are four genes encoding spore-specific nuclear LIM interactor-interacting factors (NIF proteins, a type of transcriptional regulator) that are moderately conserved in DNA sequence. NIFC1, NIFC2, and NIFC3 are zoosporogenesis-induced and grouped within 4 kb, and 20 kb away resides a sporulation-induced form, NIFS. To test the function of the NIFC family, plasmids expressing full-length hairpin constructs of NIFC1 or NIFC2 were stably transformed into P. infestans. This triggered silencing of the cognate gene in about one-third of transformants, and all three NIFC genes were usually cosilenced. However, NIFS escaped silencing despite its high sequence similarity to the NIFC genes. Silencing of the three NIFC genes impaired zoospore cyst germination by 60% but did not affect other aspects of the life cycle. Silencing was transcriptional based on nuclear run-on assays and associated with tighter chromatin packing based on nuclease accessibility experiments. The chromatin alterations extended a few hundred nucleotides beyond the boundaries of the transcribed region of the NIFC cluster and were not associated with increased DNA methylation. A plasmid expressing a short hairpin RNA having sequence similarity only to NIFC1 silenced both that gene and an adjacent member of the gene cluster, likely due to the expansion of a heterochromatic domain from the targeted locus. These data help illuminate the mechanism of silencing in Phytophthora and suggest that caution should be used when interpreting silencing experiments involving closely spaced genes.

scholarly journals Evolution of Chi motifs in Proteobacteria

2020 ◽  
Author(s):  
Angélique Buton ◽  
Louis-Marie Bobay
Keyword(s):  
Escherichia Coli ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Double Strand Breaks ◽  
Dna Double Strand Breaks ◽  
Large Dataset ◽  
High Sequence Similarity ◽  
Strand Breaks ◽  
E Coli ◽  
Dna Motif

AbstractHomologous recombination is a key pathway found in nearly all bacterial taxa. The recombination complex allows bacteria to repair DNA double strand breaks but also promotes adaption through the exchange of DNA between cells. In Proteobacteria, this process is mediated by the RecBCD complex, which relies on the recognition of a DNA motif named Chi to initiate recombination. The Chi motif has been characterized in Escherichia coli and analogous sequences have been found in several other species from diverse families, suggesting that this mode of action is widespread across bacteria. However, the sequences of Chi-like motifs are known for only five bacterial species: E. coli, Haemophilus influenzae, Bacillus subtilis, Lactococcus lactis and Staphylococcus aureus. In this study we detected putative Chi motifs in a large dataset of Proteobacteria and we identified four additional motifs sharing high sequence similarity and similar properties to the Chi motif of E. coli in 85 species of Proteobacteria. Most Chi motifs were detected in Enterobacteriaceae and this motif appears well conserved in this family. However, we did not detect Chi motifs for the majority of Proteobacteria, suggesting that different motifs are used in these species. Altogether these results substantially expand our knowledge on the evolution of Chi motifs and on the recombination process in bacteria.

scholarly journals Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli: TABLE 1

2015 ◽  
Vol 198 (1) ◽  
pp. 7-11 ◽  
Author(s):  
Regine Hengge ◽  
Michael Y. Galperin ◽  
Jean-Marc Ghigo ◽  
Mark Gomelsky ◽  
Jeffrey Green ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Mechanisms ◽  
Bacterial Species ◽  
Content Type ◽  
E Coli ◽  
Diguanylate Cyclases ◽  
Genes Encoding ◽  
Systematic Nomenclature ◽  
K 12 ◽  
Encoding Genes

In recent years,Escherichia colihas served as one of a few model bacterial species for studying cyclic di-GMP (c-di-GMP) signaling. The widely usedE. coliK-12 laboratory strains possess 29 genes encoding proteins with GGDEF and/or EAL domains, which include 12 diguanylate cyclases (DGC), 13 c-di-GMP-specific phosphodiesterases (PDE), and 4 “degenerate” enzymatically inactive proteins. In addition, six new GGDEF and EAL (GGDEF/EAL) domain-encoding genes, which encode two DGCs and four PDEs, have recently been found in genomic analyses of commensal and pathogenicE. colistrains. As a group of researchers who have been studying the molecular mechanisms and the genomic basis of c-di-GMP signaling inE. coli, we now propose a general and systematicdgcandpdenomenclature for the enzymatically active GGDEF/EAL domain-encoding genes of this model species. This nomenclature is intuitive and easy to memorize, and it can also be applied to additional genes and proteins that might be discovered in various strains ofE. coliin future studies.

scholarly journals Cloning and Characterization of the DNA Region Responsible for Megacin A-216 Production in Bacillus megaterium 216

2008 ◽  
Vol 190 (19) ◽  
pp. 6448-6457 ◽  
Author(s):  
Antal Kiss ◽  
Gabriella Balikó ◽  
Attila Csorba ◽  
Tungalag Chuluunbaatar ◽  
Katalin F. Medzihradszky ◽  
...  
Keyword(s):  
Amino Acid ◽  
Bacillus Megaterium ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Biologically Active ◽  
Mass Spectrometry Analysis ◽  
High Sequence Similarity ◽  
Spectrometry Analysis ◽  
Acid Protein ◽  
Amino Acid Protein

ABSTRACT Upon induction, Bacillus megaterium 216 produces the bacteriocin megacin A-216, which leads to lysis of the producer cell and kills B. megaterium and a few other bacterial species. The DNA region responsible for megacinogeny was cloned in B. megaterium. The nucleotide sequence of a 5,494-bp-long subfragment was determined, and the function of the genes on this fragment was studied by generating deletions and analyzing their effects on MegA phenotypes. An open reading frame (ORF) encoding a 293-amino-acid protein was identified as the gene (megA) coding for megacin A-216. BLAST searches detected sequence similarity between megacin A-216 and proteins with phospholipase A2 activity. Purified biologically active megacin A-216 preparations contained three proteins. Mass spectrometry analysis showed that the largest protein is the full-length translation product of the megA gene, whereas the two shorter proteins are fragments of the long protein created by cleavage between Gln-185 and Val-186. The molecular masses of the three polypeptides are 32,855, 21,018, and 11,855 Da, respectively. Comparison of different megacin preparations suggests that the intact chain as well as the two combined fragments can form biologically active megacin. An ORF located next to the megA gene and encoding a 91-amino-acid protein was shown to be responsible for the relative immunity displayed by the producer strain against megacin A-216. Besides the megA gene, at least two other genes, including a gene encoding a 188-amino-acid protein sharing high sequence similarity with RNA polymerase sigma factors, were shown to be required for induction of megacin A-216 expression.

scholarly journals Cloning, Biochemical Properties, and Distribution of Mycobacterial Haloalkane Dehalogenases

2005 ◽  
Vol 71 (11) ◽  
pp. 6736-6745 ◽  
Author(s):  
Andrea Jesenská ◽  
Martina Pavlová ◽  
Michal Strouhal ◽  
Radka Chaloupková ◽  
Iva Těšínská ◽  
...  
Keyword(s):  
Halogen Bond ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Maximal Activity ◽  
Biochemical Properties ◽  
Open Reading Frames ◽  
Haloalkane Dehalogenase ◽  
Ph Optimum ◽  
High Sequence Similarity ◽  
Pcr Screening

ABSTRACT Haloalkane dehalogenases are enzymes that catalyze the cleavage of the carbon-halogen bond by a hydrolytic mechanism. Genomes of Mycobacterium tuberculosis and M. bovis contain at least two open reading frames coding for the polypeptides showing a high sequence similarity with biochemically characterized haloalkane dehalogenases. We describe here the cloning of the haloalkane dehalogenase genes dmbA and dmbB from M. bovis 5033/66 and demonstrate the dehalogenase activity of their translation products. Both of these genes are widely distributed among species of the M. tuberculosis complex, including M. bovis, M. bovis BCG, M. africanum, M. caprae, M. microti, and M. pinnipedii, as shown by the PCR screening of 48 isolates from various hosts. DmbA and DmbB proteins were heterologously expressed in Escherichia coli and purified to homogeneity. The DmbB protein had to be expressed in a fusion with thioredoxin to obtain a soluble protein sample. The temperature optimum of DmbA and DmbB proteins determined with 1,2-dibromoethane is 45°C. The melting temperature assessed by circular dichroism spectroscopy of DmbA is 47°C and DmbB is 57°C. The pH optimum of DmbA depends on composition of a buffer with maximal activity at 9.0. DmbB had a single pH optimum at pH 6.5. Mycobacteria are currently the only genus known to carry more than one haloalkane dehalogenase gene, although putative haloalkane dehalogenases can be inferred in more then 20 different bacterial species by comparative genomics. The evolution and distribution of haloalkane dehalogenases among mycobacteria is discussed.

scholarly journals A ROLE OF ENVIRONMENTAL FACTORS ON CALCIUM SIGNALING GENES IN NEUROSPORA CRASSA

2015 ◽  
Vol 5 (3) ◽  
pp. 699-710
Author(s):  
Ravi Gedela
Keyword(s):  
Environmental Factors ◽  
Neurospora Crassa ◽  
Nadh Dehydrogenase ◽  
Sequence Similarity ◽  
In Silico Analysis ◽  
High Sequence Similarity ◽  
Multiple Sequence ◽  
Conserve Domain ◽  
Knockout Mutants

 Neurospora crassa possesses a complex of Ca2+_signaling system consisting of 48 Ca2+-signaling proteins.  The Ca+2-signalling  protein plays an important role in a range of processes such as a Ca2+ stress tolerance, hyphal tip branching growth, cytoskeletal organization, cell cycle progression, circadian clocks, sporulation, sexual development, and ultraviolet (uv) survival.  The environmental factors, broadly defined to include chemical, physical, nutritional, and behavioral factors...etc.  In this article, we are reporting here a role of physic-chemical environmental factors pH, glucose and ultraviolet (UV) affect on ∆NCU06366, and ∆NCU05225 Ca2+ -signaling knockout mutants in N. crassa.  The verified result showed that, ∆NCU06366 and ∆NCU05225 Ca2+ -signaling knockout mutants slower growth rate at pH (7.6), and glucose starvation against to the control wild type respectively.  In addition to that the found results showed, ultraviolet (UV) survival, there is no UV radiation affects on ∆NCU06366 and ∆NCU05225 Ca2+-signaling knockout mutants as evaluate to the positive and the negative controls in N.crassa.  Along with that, In-silico analysis Multiple sequence analysis and Phylogenetics tree for conserve domain of NCU05225 (NADH dehydrogenase) and NCU06366 (Ca2+/H+ anti-porter) Ca2+-signaling genes encodes proteins in N.crassa, showed high sequence similarity and 68-100% and 89% homology  to the other class of fungi respectively.  It indicates that, NCU05225 (Mitochondrial NADH dehydrogenase) and NCU06366 (Ca2+/H+ exchangers) Ca2+-signaling gene encoding conserve domain widespread in other class of fungi as well.   

scholarly journals Identification of Sinorhizobium melilotiGenes Regulated during Symbiosis

2000 ◽  
Vol 182 (13) ◽  
pp. 3632-3637 ◽  
Author(s):  
Didier Cabanes ◽  
Pierre Boistard ◽  
Jacques Batut
Keyword(s):  
Sinorhizobium Meliloti ◽  
Sequence Similarity ◽  
Pyruvate Dehydrogenase Complex ◽  
Surface Protein ◽  
Symbiotic Interaction ◽  
High Sequence Similarity ◽  
Copper Transporter ◽  
Genes Encoding ◽  
A Cell ◽  
Arbitrarily Primed Pcr

ABSTRACT RNA fingerprinting by arbitrarily primed PCR was used to isolateSinorhizobium meliloti genes regulated during the symbiotic interaction with alfalfa (Medicago sativa). Sixteen partial cDNAs were isolated whose corresponding genes were differentially expressed between symbiotic and free-living conditions. Thirteen sequences corresponded to genes up-regulated during symbiosis, whereas three were instead repressed during establishment of the symbiotic interaction. Seven cDNAs corresponded to known or predictednif and fix genes. Four presented high sequence similarity with genes not yet identified in S. meliloti, including genes encoding a component of the pyruvate dehydrogenase complex, a cell surface protein component, a copper transporter, and an argininosuccinate lyase. Finally, five cDNAs did not exhibit any similarity with sequences present in databases. A detailed expression analysis of the nine non-nif-fix genes provided evidence for an unexpected variety of regulatory patterns, most of which have not been described so far.

scholarly journals Characterisation and Mutagenesis Study of An Alternative Sigma Factor Gene (hrpL) from Erwinia mallotivora Reveal Its Central Role in Papaya Dieback Disease

Biology ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 323
Author(s):  
Amin-Asyraf Tamizi ◽  
Norliza Abu-Bakar ◽  
Aimera-Farhana Samsuddin ◽  
Lina Rozano ◽  
Rohaiza Ahmad-Redzuan ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
High Sequence Similarity ◽  
Protein Protein Interaction ◽  
Nucleotide Sequence Alignment ◽  
Σ Factor ◽  
Dieback Disease ◽  
Mutagenesis Study ◽  
Sigma 70

The alternative sigma (σ) factor E, RpoE or HrpL, has been reported to be involved in stress- and pathogenicity-related transcription initiation in Escherichia coli and many other Gram-negative bacteria, including Erwinia spp. and Pseudomonas spp. A previous study identified the hrpL/rpoE transcript as one of the significant differentially expressed genes (DEGs) during early E. mallotivora infection in papaya and those data serve as the basis of the current project. Here, the full coding DNA sequence (CDS) of hrpL from E. mallotivora (EmhrpL) was determined to be 549 bp long, and it encoded a 21.3 kDa HrpL protein that possessed two highly conserved sigma-70 (σ70) motifs—σR2 and σR4. Nucleotide sequence alignment revealed the hrpL from E. mallotivora shared high sequence similarity to rpoE/hrpL from E. tracheiphila (83%), E. pyrifoliae (81%), and E. tasmaniensis (80%). Phylogenetics analysis indicated hrpL from E. mallotivora to be monophyletic with rpoEs/hrpLs from Pantoea vagans, E. herbicola, and E. tracheiphila. Structural analysis postulated that the E. mallotivora’s alternative σ factor was non-transmembranic and was an extracytoplasmic function (ECF) protein—characteristics shared by other σ factors in different bacterial species. Notably, the protein–protein interaction (PPI) study through molecular docking suggested the σ factor could be possibly inhibited by an anti-σ. Finally, a knockout of hrpL in E. mallotivora (ΔEmhrpL) resulted in avirulence in four-month-old papaya plants. These findings have revealed that the hrpL is a necessary element in E. mallotivora pathogenicity and also predicted that the gene can be inhibited by an anti-σ.

scholarly journals Functional Analysis of Genes in the rfbLocus of Leptospira borgpetersenii Serovar Hardjo Subtype Hardjobovis

2000 ◽  
Vol 68 (7) ◽  
pp. 3793-3798 ◽  
Author(s):  
Dieter M. Bulach ◽  
Thareerat Kalambaheti ◽  
Alejandro de la Peña-Moctezuma ◽  
Ben Adler
Keyword(s):  
Sequence Similarity ◽  
Bacterial Species ◽  
Open Reading Frames ◽  
New Host ◽  
E Coli ◽  
Serovar Typhimurium ◽  
Genes Encoding ◽  
Leptospira Borgpetersenii ◽  
Nucleotide Sugars

ABSTRACT Lipopolysaccharide (LPS) is a key antigen in immunity to leptospirosis. Its biosynthesis requires enzymes for the biosynthesis and polymerization of nucleotide sugars and the transport through and attachment to the bacterial membrane. The genes encoding these functions are commonly clustered into loci; for Leptospira borgpetersenii serovar Hardjo subtype Hardjobovis, this locus, named rfb, spans 36.7 kb and contains 31 open reading frames, of which 28 have been assigned putative functions on the basis of sequence similarity. Characterization of the function of these genes is hindered by the fact that it is not possible to construct isogenic mutant strains in Leptospira. We used two approaches to circumvent this problem. The first was to clone the entire locus into a heterologous host system and determine if a “recombinant” LPS or polysaccharide was synthesized in the new host. The second approach used putative functions to identify mutants in other bacterial species whose mutations might be complemented by genes on the leptospiralrfb locus. This approach was used to investigate the function of three genes in the leptospiral rfb locus and demonstrated function for orfH10, which complemented awbpM strain of Pseudomonas aeruginosa, andorfH13, which complemented an rfbW strain ofVibrio cholerae. However, despite the similarity of OrfH11 to WecC, a wecC strain of E. coli was not complemented by orfH11. The predicted protein encoded byorfH8 is similar to GalE from a number of organisms. ASalmonella enterica serovar Typhimurium strain producing no GalE was used as a background in which orfH8 produced detectable GalE enzyme activity.

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