scholarly journals Identification and Characterization of a Putative Transcriptional Regulator Controlling the Expression of Fouling Inhibitors in Pseudoalteromonas tunicata

2002 ◽  
Vol 68 (1) ◽  
pp. 372-378 ◽  
Author(s):  
Suhelen Egan ◽  
Sally James ◽  
Staffan Kjelleberg
Keyword(s):  
Marine Invertebrate ◽  
Sequence Similarity ◽  
Polyacrylamide Gel Electrophoresis ◽  
Regulatory Elements ◽  
Regulation Of Expression ◽  
High Sequence Similarity ◽  
Antifouling Activity ◽  
Pseudoalteromonas Tunicata ◽  
Fouling Organisms

ABSTRACT The dark green pigmented marine bacterium Pseudoalteromonas tunicata colonizes living surfaces and produces a range of extracellular compounds that inhibit common fouling organisms, including marine invertebrate larvae, algae, bacteria, and fungi. We have observed a positive correlation between the antifouling activity of P. tunicata strain D2 and the expression of pigmentation. To address the hypothesis that pigmentation and antifouling may be jointly regulated in this organism and to begin to identify potential regulatory elements, we used transposon mutagenesis to generate a strain of P. tunicata deficient in antifouling activity. The data presented here describe the phenotypic and molecular characterization of a nonpigmented transposon mutant strain of P. tunicata (D2W2). Analyses of the antifouling capabilities of D2W2 demonstrate that this strain is deficient in the ability to inhibit each of the target fouling organisms. Genetic analysis of D2W2 identified a gene, designated wmpR (white mutant phenotype), with high sequence similarity to transcriptional regulators ToxR from Vibrio cholerae and CadC from Escherichia coli. Two-dimensional polyacrylamide gel electrophoresis analysis revealed that WmpR is essential for the expression of a significant subset of stationary-phase-induced proteins likely to be important for the synthesis of fouling inhibitors. The identification of a gene involved in the regulation of expression of antifouling phenotypes will contribute to the understanding of the interactions between bacteria and other surface-colonizing organisms in the marine environment.

scholarly journals Tuning the ion selectivity of two-pore channels

2017 ◽  
Vol 114 (5) ◽  
pp. 1009-1014 ◽  
Author(s):  
Jiangtao Guo ◽  
Weizhong Zeng ◽  
Youxing Jiang
Keyword(s):  
Sequence Similarity ◽  
Ion Selectivity ◽  
Structural Basis ◽  
Monovalent Cations ◽  
Nonselective Cation Channel ◽  
High Sequence Similarity ◽  
Selective Channel ◽  
Tm Domain ◽  
Key Residues

Organellar two-pore channels (TPCs) contain two copies of aShaker-like six-transmembrane (6-TM) domain in each subunit and are ubiquitously expressed in plants and animals. Interestingly, plant and animal TPCs share high sequence similarity in the filter region, yet exhibit drastically different ion selectivity. Plant TPC1 functions as a nonselective cation channel on the vacuole membrane, whereas mammalian TPC channels have been shown to be endo/lysosomal Na+-selective or Ca2+-release channels. In this study, we performed systematic characterization of the ion selectivity of TPC1 fromArabidopsis thaliana(AtTPC1) and compared its selectivity with the selectivity of human TPC2 (HsTPC2). We demonstrate that AtTPC1 is selective for Ca2+over Na+, but nonselective among monovalent cations (Li+, Na+, and K+). Our results also confirm that HsTPC2 is a Na+-selective channel activated by phosphatidylinositol 3,5-bisphosphate. Guided by our recent structure of AtTPC1, we converted AtTPC1 to a Na+-selective channel by mimicking the selectivity filter of HsTPC2 and identified key residues in the TPC filters that differentiate the selectivity between AtTPC1 and HsTPC2. Furthermore, the structure of the Na+-selective AtTPC1 mutant elucidates the structural basis for Na+selectivity in mammalian TPCs.

scholarly journals O-Acetylserine Sulfhydrylase fromMethanosarcina thermophila

2000 ◽  
Vol 182 (1) ◽  
pp. 45-50 ◽  
Author(s):  
Birthe Borup ◽  
James G. Ferry
Keyword(s):  
Specific Activity ◽  
Sequence Similarity ◽  
Polyacrylamide Gel Electrophoresis ◽  
Substrate Inhibition ◽  
Sodium Dodecyl ◽  
Gel Filtration ◽  
Cysteine Biosynthesis ◽  
High Sequence Similarity ◽  
Methanosarcina Thermophila ◽  
Moderately Thermophilic

ABSTRACT Cysteine is the major source of fixed sulfur for the synthesis of sulfur-containing compounds in organisms of the Bacteriaand Eucarya domains. Though pathways for cysteine biosynthesis have been established for both of these domains, it is unknown how the Archaea fix sulfur or synthesize cysteine. None of the four archaeal genomes sequenced to date contain open reading frames with identities to eitherO-acetyl-l-serine sulfhydrylase (OASS) or homocysteine synthase, the only sulfur-fixing enzymes known in nature. We report the purification and characterization of OASS from acetate-grown Methanosarcina thermophila, a moderately thermophilic methanoarchaeon. The purified OASS contained pyridoxal 5′-phosphate and catalyzed the formation of l-cysteine and acetate from O-acetyl-l-serine and sulfide. The N-terminal amino acid sequence has high sequence similarity with other known OASS enzymes from the Eucarya andBacteria domains. The purified OASS had a specific activity of 129 μmol of cysteine/min/mg, with a Km of 500 ± 80 μM for sulfide, and exhibited positive cooperativity and substrate inhibition withO-acetyl-l-serine. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a single band at 36 kDa, and native gel filtration chromatography indicated a molecular mass of 93 kDa, suggesting that the purified OASS is either a homodimer or a homotrimer. The optimum temperature for activity was between 40 and 60°C, consistent with the optimum growth temperature for M. thermophila. The results of this study provide the first evidence for a sulfur-fixing enzyme in the Archaea domain. The results also provide the first biochemical evidence for an enzyme with the potential for involvement in cysteine biosynthesis in theArchaea.

scholarly journals Inheritance of seedlessness and the molecular characterization of the INO gene in Annonaceae

2023 ◽  
Vol 83 ◽  
Author(s):  
B. R. R. M. Nassau ◽  
P. S. C. Mascarenhas ◽  
A. G. Guimarães ◽  
F. M. Feitosa ◽  
H. M. Ferreira ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Type A ◽  
Molecular Techniques ◽  
Wild Type ◽  
Annona Squamosa ◽  
High Sequence Similarity ◽  
Breeding Programs ◽  
Complete Dominance ◽  
Young Leaves

Abstract The inheritance of the seedless fruit characteristic of Annona squamosa has not yet been explained. Molecular techniques may aid breeding programs, mainly in the assisted selection of the target gene. The INO gene may be related to seed development in these fruits. The objective of the present paper was to investigate the inheritance of seedlessness in the 'Brazilian seedless' sugar apple and INO gene conservation in Annona squamosa and Annona cherimola x Annona squamosa genotypes by assessing their homology with the INO database genes. The F1 generation was obtained by crossing the mutant 'Brazilian seedless' (male genitor) (P1) with the wild-type A. squamosa with seeds (M1 and M2, female genitors). The INO gene was studied in mutant and wild-type A. squamosa (P1, M1, M2 and M3) and in the Gefner atemoya (A. cherimola x A. squamosa) (M4) cultivar. The DNA was extracted from young leaves, and four sets of specific primers flanking the INO gene were amplified. The seedless characteristic was identified as stenospermatic in the fruits of parental P1, suggesting monogenic inheritance with complete dominance. High sequence similarity of the INO gene amplifications in the sugar apple accessions (M1, M2, M3) and the atemoya cultivar Gefner (M4) reinforces the hypothesis of their conservation.

scholarly journals Isolation and Characterization of Insecticidal Toxins from the Venom of the North African Scorpion, Buthacus leptochelys

Toxins ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 236 ◽  
Author(s):  
Yusuke Yoshimoto ◽  
Masahiro Miyashita ◽  
Mohammed Abdel-Wahab ◽  
Moustafa Sarhan ◽  
Yoshiaki Nakagawa ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Scorpion Venom ◽  
Spectrometric Analysis ◽  
North African ◽  
High Sequence Similarity ◽  
The North ◽  
Isolation And Characterization ◽  
Ms Analysis ◽  
Insect Toxicity

Various bioactive peptides have been identified in scorpion venom, but there are many scorpion species whose venom has not been investigated. In this study, we characterized venom components of the North African scorpion, Buthacus leptochelys, by mass spectrometric analysis and evaluated their insect toxicity. This is the first report of chemical and biological characterization of the B. leptochelys venom. LC/MS analysis detected at least 148 components in the venom. We isolated four peptides that show insect toxicity (Bl-1, Bl-2, Bl-3, and Bl-4) through bioassay-guided HPLC fractionation. These toxins were found to be similar to scorpion α- and β-toxins based on their N-terminal sequences. Among them, the complete primary structure of Bl-1 was determined by combination of Edman degradation and MS/MS analysis. Bl-1 is composed of 67 amino acid residues and crosslinked with four disulfide bonds. Since Bl-1 shares high sequence similarity with α-like toxins, it is likely that it acts on Na+ channels of both insects and mammals.

scholarly journals Regulation of a New Cell Wall Hydrolase Gene,cwlF, Which Affects Cell Separation in Bacillus subtilis

1998 ◽  
Vol 180 (9) ◽  
pp. 2549-2555 ◽  
Author(s):  
Shu Ishikawa ◽  
Yoshiko Hara ◽  
Ryo Ohnishi ◽  
Junichi Sekiguchi
Keyword(s):  
Cell Wall ◽  
Bacillus Subtilis ◽  
Rna Polymerase ◽  
Sequence Similarity ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Exponential Growth Phase ◽  
High Sequence Similarity ◽  
Cell Wall Hydrolase ◽  
Mutant Cells

ABSTRACT Bacillus subtilis produces a 35-kDa cell wall hydrolase, CwlF, during vegetative growth. The CwlF protein was extracted from B. subtilis cwlB sigD mutant cells and separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. N-terminal amino acid sequencing revealed that its sequence is completely identical to that of the internal region of thepapQ gene product. Disruption of the papQ gene in the B. subtilis chromosome led to the complete loss of CwlF, indicating that papQ is identical tocwlF. CwlF exhibits high sequence similarity to the p60 proteins of Listeria species, NlpC proteins ofEscherichia coli and Haemophilus influenzae, and Enp2 protein of Bacillus sphaericus. The β-galactosidase activity of the cwlF-lacZ transcriptional fusion and Northern blot analysis of the cwlF gene indicated that the gene is expressed as a monocistronic operon during the exponential growth phase, and primer extension analysis suggested that the cwlF gene is transcribed mainly by EςA RNA polymerase and weakly by EςH RNA polymerase. While the cells of the cwlF-deficient mutant were about twice as long as those of the wild-type strain, the cwlF sigD double mutant cells exhibited extraordinary microfiber formation, in contrast to the filamentation of the sigD mutant. The CwlF production was not affected by the pleiotropic mutationsflaD1 and degU32(Hy), which endow cells with the ability of extensive filamentation.

scholarly journals Isolation and structural characterization of insulin and glucagon from the holocephalan species Callorhynchus milii (elephantfish)

1989 ◽  
Vol 263 (1) ◽  
pp. 261-266 ◽  
Author(s):  
B C Berks ◽  
C J Marshall ◽  
A Carne ◽  
S M Galloway ◽  
J F Cutfield
Keyword(s):  
Gas Phase ◽  
Receptor Binding ◽  
Structural Characterization ◽  
Sequence Similarity ◽  
Cartilaginous Fish ◽  
Proteolytic Processing ◽  
Reverse Phase ◽  
High Sequence Similarity ◽  
Processing Mechanisms

Both insulin and glucagon from the pancreas of the holocephalan cartilaginous fish Callorhynchus milii (elephantfish) have been isolated and purified. Two reverse-phase h.p.l.c. steps enabled recovery of sufficient material for gas-phase sequencing of the intact chains as well as peptide digestion products. The elephantfish insulin sequence shows 14 differences from pig insulin, including two unusual substitutions, Val-A14 and Gln-B30, though none of these is thought likely to influence receptor binding significantly. The insulin B-chain contains 31 residues, one more than mammalian insulins, but markedly less than that of the closely related ratfish with which it otherwise exhibits high sequence similarity. Elephantfish and pig glucagons differ at only four positions, but there are six changes from the ratfish glucagon-36 (normal glucagon contains 29 residues) sequence. It is apparent that different prohormone proteolytic processing mechanisms operate in the two holocephalan species.

scholarly journals The Isolation of Pyrroloformamide Congeners and Characterization of Its Biosynthetic Gene Cluster from Streptomyces sp. CB02980 Revealed a Unified Mechanism for Dithiolopyrrolone Biosynthesis

2019 ◽  
Author(s):  
Wenqing Zhou ◽  
Haoyu Liang ◽  
Xiangjing Qin ◽  
Danfeng Cao ◽  
Xiangcheng Zhu ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Sequence Similarity ◽  
Biosynthetic Gene Cluster ◽  
Gene Replacement ◽  
Biosynthetic Gene ◽  
High Sequence Similarity ◽  
Bicyclic Structure ◽  
Microbial Natural Products ◽  
Drug Leads

Dithiolopyrrolones are microbial natural products containing a disulfide or thiosulfonate bridge embedded in a unique bicyclic structure. In the current study, two new dithiolopyrrolones, pyrroloformamide C (<b>3</b>) and pyrroloformamide D (<b>4</b>), were isolated from <i>Streptomyces </i>sp. CB02980, together with the known pyrroloformamides <b>1 </b>and <b>2</b>. The biosynthetic gene cluster for pyrroloformamides was identified from <i>S</i>. sp. CB02980, which shared high sequence similarity with those of dithiolopyrrolones, including holomycin and thiolutin. Gene replacement of pyfE, which encodes a non-ribosomal peptide synthetase, abolished the production of <b>1</b>－<b>4</b>. Overexpression of <i>pyfN</i>, a type II thioesterase gene, increased the production of <b>1</b> and <b>2</b>. The structure elucidation and biosynthetic characterization of pyrroloformamides <b>1</b> - <b>4</b> may inspire future efforts to discover new dithiolopyrrolones, which are promising drug leads for the treatment of infectious diseases or cancer.

scholarly journals A pan-cancer landscape of somatic substitutions in non-unique regions of the human genome

2020 ◽  
Author(s):  
Maxime Tarabichi ◽  
Jonas Demeulemeester ◽  
Annelien Verfaillie ◽  
Adrienne M. Flanagan ◽  
Peter Van Loo ◽  
...  
Keyword(s):  
Human Genome ◽  
Sequence Similarity ◽  
Gene Families ◽  
Regulatory Elements ◽  
Cancer Genes ◽  
Mutation Load ◽  
Sequencing Data ◽  
High Sequence Similarity ◽  
Computational Analyses ◽  
Pan Cancer

AbstractAround 13% of the human genome displays high sequence similarity with at least one other chromosomal position and thereby poses challenges for computational analyses such as detection of somatic events in cancer. We here extract features of sequencing data from across non-unique regions and employ a machine learning pipeline to describe a landscape of somatic substitutions in 2,658 cancers from the PCAWG cohort. We show mutations in non-unique regions are consistent with mutations in unique regions in terms of mutation load and substitution profiles, and can be validated with linked-read sequencing. This uncovers hidden mutations in ~1,700 coding sequences and thousands of regulatory elements, including known cancer genes, immunoglobulins, and highly mutated gene families.

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