scholarly journals Bacillus subtilis promoter sequences data set for promoter prediction in Gram-positive bacteria

Data in Brief ◽  
2018 ◽  
Vol 19 ◽  
pp. 264-270 ◽  
Author(s):  
Rafael Vieira Coelho ◽  
Scheila de Avila e Silva ◽  
Sergio Echeverrigaray ◽  
Ana Paula Longaray Delamare
Keyword(s):  
Bacillus Subtilis ◽  
Promoter Prediction ◽  
Gram Positive ◽  
Data Set ◽  
Promoter Sequences ◽  
Gram Positive Bacteria

scholarly journals In Vitro Characterization of the Bacillus subtilis Protein Tyrosine Phosphatase YwqE

2005 ◽  
Vol 187 (10) ◽  
pp. 3384-3390 ◽  
Author(s):  
Ivan Mijakovic ◽  
Lucia Musumeci ◽  
Lutz Tautz ◽  
Dina Petranovic ◽  
Robert A. Edwards ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Tyrosine Phosphatase ◽  
Protein Tyrosine Phosphatases ◽  
Class Ii ◽  
Gram Positive ◽  
Protein Tyrosine ◽  
Gram Positive Bacteria ◽  
New Family ◽  
In Vitro Characterization

ABSTRACT Both gram-negative and gram-positive bacteria possess protein tyrosine phosphatases (PTPs) with a catalytic Cys residue. In addition, many gram-positive bacteria have acquired a new family of PTPs, whose first characterized member was CpsB from Streptococcus pneumoniae. Bacillus subtilis contains one such CpsB-like PTP, YwqE, in addition to two class II Cys-based PTPs, YwlE and YfkJ. The substrates for both YwlE and YfkJ are presently unknown, while YwqE was shown to dephosphorylate two phosphotyrosine-containing proteins implicated in UDP-glucuronate biosynthesis, YwqD and YwqF. In this study, we characterize YwqE, compare the activities of the three B. subtilis PTPs (YwqE, YwlE, and YfkJ), and demonstrate that the two B. subtilis class II PTPs do not dephosphorylate the physiological substrates of YwqE.

scholarly journals A Conserved Class II Type Thioester Domain-Containing Adhesin Is Required for Efficient Conjugation in Bacillus subtilis

mBio ◽  
2021 ◽  
Vol 12 (2) ◽  
Author(s):  
César Gago-Córdoba ◽  
Jorge Val-Calvo ◽  
David Abia ◽  
Alberto Díaz-Talavera ◽  
Andrés Miguel-Arribas ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Bacillus Subtilis ◽  
Recipient Cell ◽  
Class Ii ◽  
Pair Formation ◽  
Conjugative Plasmid ◽  
Mating Pair ◽  
Gram Positive ◽  
Content Type ◽  
Gram Positive Bacteria

ABSTRACT Conjugation, the process by which a DNA element is transferred from a donor to a recipient cell, is the main horizontal gene transfer route responsible for the spread of antibiotic resistance and virulence genes. Contact between a donor and a recipient cell is a prerequisite for conjugation, because conjugative DNA is transferred into the recipient via a channel connecting the two cells. Conjugative elements encode proteins dedicated to facilitating the recognition and attachment to recipient cells, also known as mating pair formation. A subgroup of the conjugative elements is able to mediate efficient conjugation during planktonic growth, and mechanisms facilitating mating pair formation will be particularly important in these cases. Conjugative elements of Gram-negative bacteria encode conjugative pili, also known as sex pili, some of which are retractile. Far less is known about mechanisms that promote mating pair formation in Gram-positive bacteria. The conjugative plasmid pLS20 of the Gram-positive bacterium Bacillus subtilis allows efficient conjugation in liquid medium. Here, we report the identification of an adhesin gene in the pLS20 conjugation operon. The N-terminal region of the adhesin contains a class II type thioester domain (TED) that is essential for efficient conjugation, particularly in liquid medium. We show that TED-containing adhesins are widely conserved in Gram-positive bacteria, including pathogens where they often play crucial roles in pathogenesis. Our study is the first to demonstrate the involvement of a class II type TED-containing adhesin in conjugation. IMPORTANCE Bacterial resistance to antibiotics has become a serious health care problem. The spread of antibiotic resistance genes between bacteria of the same or different species is often mediated by a process named conjugation, where a donor cell transfers DNA to a recipient cell through a connecting channel. The first step in conjugation is recognition and attachment of the donor to a recipient cell. Little is known about this first step, particularly in Gram-positive bacteria. Here, we show that the conjugative plasmid pLS20 of Bacillus subtilis encodes an adhesin protein that is essential for effective conjugation. This adhesin protein has a structural organization similar to adhesins produced by other Gram-positive bacteria, including major pathogens, where the adhesins serve in attachment to host tissues during colonization and infection. Our findings may thus also open novel avenues to design drugs that inhibit the spread of antibiotic resistance by blocking the first recipient-attachment step in conjugation.

scholarly journals Bacillus subtilis YhaM, a Member of a New Family of 3′-to-5′ Exonucleases in Gram-Positive Bacteria

2002 ◽  
Vol 184 (22) ◽  
pp. 6250-6259 ◽  
Author(s):  
Irina A. Oussenko ◽  
Roberto Sanchez ◽  
David H. Bechhofer
Keyword(s):  
Bacillus Subtilis ◽  
Mrna Turnover ◽  
Wild Type ◽  
Rnase R ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
New Family ◽  
Double Stranded Dna ◽  
Ob Fold ◽  
Related Proteins

ABSTRACT A strain of Bacillus subtilis lacking two 3′-to-5′ exoribonucleases, polynucleotide phosphorylase (PNPase) and RNase R, was used to purify another 3′-to-5′ exoribonuclease, which is encoded by the yhaM gene. YhaM was active in the presence of Mn2+ (or Co2+), was inactive in the presence of Mg2+, and could also degrade single-stranded DNA. The half-life of bulk mRNA in a mutant lacking PNPase, RNase R, and YhaM was not significantly different from that of the wild type, suggesting the existence of additional activities that can participate in mRNA turnover. Sequence homologues of YhaM were found only in gram-positive organisms. The Staphylococcus aureus homologue, CBF1, which had been characterized as a double-stranded DNA binding protein involved in plasmid replication, was also shown to be an Mn2+-dependent exoribonuclease. YhaM protein has a C-terminal “HD domain,” found in metal-dependent phosphohydrolases. By structure modeling, it was shown that YhaM also contains an N-terminal “OB-fold,” present in many oligosaccharide- and oligonucleotide-binding proteins. The combination of these two domains is unique. Thus, YhaM and 10 related proteins from gram-positive organisms constitute a new exonuclease family.

CtaG is required for formation of active cytochrome c oxidase in Bacillus subtilis

Microbiology ◽  
2004 ◽  
Vol 150 (2) ◽  
pp. 415-425 ◽  
Author(s):  
Jenny Bengtsson ◽  
Claes von Wachenfeldt ◽  
Lena Winstedt ◽  
Per Nygaard ◽  
Lars Hederstedt
Keyword(s):  
Bacillus Subtilis ◽  
Copper Ions ◽  
Eukaryotic Cells ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Assembly Factor ◽  
Membrane Bound ◽  
Respiratory Oxidases ◽  
Copper Centre

The Gram-positive bacterium Bacillus subtilis contains two respiratory oxidases of the haem-copper superfamily: cytochrome aa 3, which is a quinol oxidase, and cytochrome caa 3, which is a cytochrome c oxidase. Cytochrome c oxidase uniquely contains a di-copper centre, CuA. B. subtilis CtaG is a membrane protein encoded by the same gene cluster as that which encodes the subunits of cytochrome c oxidase. The role of B. subtilis CtaG and orthologous proteins present in many other Gram-positive bacteria has remained unexplored. The sequence of CtaG is unrelated to that of CtaG/Cox11p of proteobacteria and eukaryotic cells. This study shows that B. subtilis CtaG is essential for the formation of active cytochrome caa 3 but is not required for assembly of the core subunits I and II with haem in the membrane and it has no role in the synthesis of active cytochrome aa 3. B. subtilis YpmQ, a homologue to Sco1p of eukaryotic cells, is also a membrane-bound cytochrome c oxidase-specific assembly factor. Properties of CtaG- and YpmQ-deficient mutants were compared. Cells lacking YpmQ showed a low cytochrome c oxidase activity and this defect was suppressed by the supplementation of the growth medium with copper ions. It has previously been proposed that YpmQ/Sco1p is involved in synthesis of the CuA centre. The results of this study are consistent with this proposal but the exact role of YpmQ in assembly of cytochrome c oxidase remains to be elucidated.

scholarly journals The First Structure of a Lantibiotic Immunity Protein, SpaI from Bacillus subtilis, Reveals a Novel Fold

2012 ◽  
Vol 287 (42) ◽  
pp. 35286-35298 ◽  
Author(s):  
Nina A. Christ ◽  
Sophie Bochmann ◽  
Daniel Gottstein ◽  
Elke Duchardt-Ferner ◽  
Ute A. Hellmich ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Lipid Membranes ◽  
Biologically Active ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Lipid Ii ◽  
Terminal Fragment ◽  
Terminal Amino ◽  
Immunity Mechanism ◽  
Producer Strains

Lantibiotics are peptide-derived antibiotics that inhibit the growth of Gram-positive bacteria via interactions with lipid II and lipid II-dependent pore formation in the bacterial membrane. Due to their general mode of action the Gram-positive producer strains need to express immunity proteins (LanI proteins) for protection against their own lantibiotics. Little is known about the immunity mechanism protecting the producer strain against its own lantibiotic on the molecular level. So far, no structures have been reported for any LanI protein. We solved the structure of SpaI, a LanI protein from the subtilin producing strain Bacillus subtilis ATCC 6633. SpaI is a 16.8-kDa lipoprotein that is attached to the outside of the cytoplasmic membrane via a covalent diacylglycerol anchor. SpaI together with the ABC transporter SpaFEG protects the B. subtilis membrane from subtilin insertion. The solution-NMR structure of a 15-kDa biologically active C-terminal fragment reveals a novel fold. We also demonstrate that the first 20 N-terminal amino acids not present in this C-terminal fragment are unstructured in solution and are required for interactions with lipid membranes. Additionally, growth tests reveal that these 20 N-terminal residues are important for the immunity mediated by SpaI but most likely are not part of a possible subtilin binding site. Our findings are the first step on the way of understanding the immunity mechanism of B. subtilis in particular and of other lantibiotic producing strains in general.

scholarly journals In SilicoEvidence for the Horizontal Transfer ofgsiB, a σΒ-Regulated Gene in Gram-Positive Bacteria, to Lactic Acid Bacteria

2011 ◽  
Vol 77 (10) ◽  
pp. 3526-3531 ◽  
Author(s):  
Ioanna-Areti Asteri ◽  
Effrossyni Boutou ◽  
Rania Anastasiou ◽  
Bruno Pot ◽  
Constantinos E. Vorgias ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Horizontal Transfer ◽  
In Silico ◽  
Glucose Starvation ◽  
Gram Positive ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Inducible Protein

ABSTRACTgsiB, coding for glucose starvation-inducible protein B, is a characteristic member of the σΒstress regulon ofBacillus subtilisand several other Gram-positive bacteria. Here we providein silicoevidence for the horizontal transfer ofgsiBin lactic acid bacteria that are devoid of the σΒfactor.

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