Genomes and Genes
Summary: Proteins found in any species of bacterium.
- Foster T, Geoghegan J, Ganesh V, Hook M. Adhesion, invasion and evasion: the many functions of the surface proteins of Staphylococcus aureus. Nat Rev Microbiol. 2014;12:49-62 pubmed publisher..Thus, cell wall-anchored proteins are essential virulence factors for the survival of S. aureus in the commensal state and during invasive infections, and targeting them with vaccines could combat S. aureus infections. ..
- Liu S, Lockless S. Equilibrium selectivity alone does not create K+-selective ion conduction in K+ channels. Nat Commun. 2013;4:2746 pubmed publisher..Thus, the detailed architecture of the K(+) channel selectivity filter, and not only its equilibrium ion preference, is fundamental to the generation of selectivity during ion conduction. ..
- Yu X, Wen Z, Chen G, Li R, Ding B, Yao Y, et al. Molecular characterization of multidrug-resistant Mycobacterium tuberculosis isolated from south-central in China. J Antibiot (Tokyo). 2014;67:291-7 pubmed publisher..An understanding of the mutations in these drug-resistant strains may aid in choosing the appropriate chemotherapy regimens on the pharmacogenetic properties of the mutations for the prevention and control of tuberculosis. ..
- Wirthmueller L, Maqbool A, Banfield M. On the front line: structural insights into plant-pathogen interactions. Nat Rev Microbiol. 2013;11:761-76 pubmed publisher..In this Review, we summarize the key developments in the structural biology of plant pathogen-host interactions. ..
- Guilfoyle A, Deshpande C, Vincent K, Pedroso M, Schenk G, Maher M, et al. Structural and functional analysis of a FeoB A143S G5 loop mutant explains the accelerated GDP release rate. FEBS J. 2014;281:2254-65 pubmed publisher..We conclude that the identity of the residue at this position in the G5 loop plays a key role in the nucleotide release rate by allowing the correct positioning and hydrogen bonding of the nucleotide base. ..
- Laganowsky A, Reading E, Allison T, Ulmschneider M, Degiacomi M, Baldwin A, et al. Membrane proteins bind lipids selectively to modulate their structure and function. Nature. 2014;510:172-175 pubmed publisher..We anticipate that these findings will be important not only for defining the selectivity of membrane proteins towards lipids, but also for understanding the role of lipids in modulating protein function or drug binding. ..
- Natale A, Duplantis J, Piasta K, Falke J. Structure, function, and on-off switching of a core unit contact between CheA kinase and CheW adaptor protein in the bacterial chemosensory array: A disulfide mapping and mutagenesis study. Biochemistry. 2013;52:7753-65 pubmed publisher..In principle, this signal could spread out into the surrounding array via the kinase-adaptor ring, employing a series of alternating frozen-dynamic transitions that transmit low-energy attractant signals long distances...
- Plano G, Schesser K. The Yersinia pestis type III secretion system: expression, assembly and role in the evasion of host defenses. Immunol Res. 2013;57:237-45 pubmed publisher..Within the host cell, the Yop effector proteins function to inhibit bacterial phagocytosis and to suppress the production of pro-inflammatory cytokines. ..
- Gwynn E, Smith A, Guy C, Savery N, McGlynn P, Dillingham M. The conserved C-terminus of the PcrA/UvrD helicase interacts directly with RNA polymerase. PLoS ONE. 2013;8:e78141 pubmed publisher..A disordered but highly conserved C-terminal region of PcrA, which distinguishes PcrA/UvrD from otherwise related enzymes such as Rep, is both necessary and sufficient for interaction with RNA polymerase. ..
- Saleh M, Bartual S, Abdullah M, Jensch I, Asmat T, Petruschka L, et al. Molecular architecture of Streptococcus pneumoniae surface thioredoxin-fold lipoproteins crucial for extracellular oxidative stress resistance and maintenance of virulence. EMBO Mol Med. 2013;5:1852-70 pubmed publisher..Identification of this system and its target proteins paves the way for the design of novel antimicrobials. ..
- Loose M, Mitchison T. The bacterial cell division proteins FtsA and FtsZ self-organize into dynamic cytoskeletal patterns. Nat Cell Biol. 2014;16:38-46 pubmed publisher..Our findings provide a model for the initial steps of bacterial cell division and illustrate how dynamic polymers can self-organize into large-scale structures. ..
- Pontikis K, Karaiskos I, Bastani S, Dimopoulos G, Kalogirou M, Katsiari M, et al. Outcomes of critically ill intensive care unit patients treated with fosfomycin for infections due to pandrug-resistant and extensively drug-resistant carbapenemase-producing Gram-negative bacteria. Int J Antimicrob Agents. 2014;43:52-9 pubmed publisher..Resistance development during therapy, which has been a matter of concern in previous studies, did not occur frequently. The necessity of combination with other antibiotics requires further investigation...
- Anders K, Daminelli Widany G, Mroginski M, von Stetten D, Essen L. Structure of the cyanobacterial phytochrome 2 photosensor implies a tryptophan switch for phytochrome signaling. J Biol Chem. 2013;288:35714-25 pubmed publisher..This "Trp switch" is supposed to be a crucial element for the photochromicity of all multidomain phytochromes. ..
- Marini G, Luchese M, Argondizzo A, de Góes A, Galler R, Alves T, et al. Experimental design approach in recombinant protein expression: determining medium composition and induction conditions for expression of pneumolysin from Streptococcus pneumoniae in Escherichia coli and preliminary purification process. BMC Biotechnol. 2014;14:1 pubmed publisher..One of the most prominent proteins is pneumolysin (Ply), present in almost all the serotypes known at the moment, which shows an effective protection against S. pneumoniae infections...
- O Loughlin C, Miller L, Siryaporn A, Drescher K, Semmelhack M, Bassler B. A quorum-sensing inhibitor blocks Pseudomonas aeruginosa virulence and biofilm formation. Proc Natl Acad Sci U S A. 2013;110:17981-6 pubmed publisher..Because LasR and RhlR reciprocally control crucial virulence factors, appropriately tuning rather than completely inhibiting their activities appears to hold the key to blocking pathogenesis in vivo. ..
- Hofbauer S, Gruber C, Pirker K, Sündermann A, Schaffner I, Jakopitsch C, et al. Transiently produced hypochlorite is responsible for the irreversible inhibition of chlorite dismutase. Biochemistry. 2014;53:3145-57 pubmed publisher..We discuss the role of distal Arg173 by keeping hypochlorite in the reaction sphere for O-O bond formation. ..
- Zumbo A, Palucci I, Cascioferro A, Sali M, Ventura M, D Alfonso P, et al. Functional dissection of protein domains involved in the immunomodulatory properties of PE_PGRS33 of Mycobacterium tuberculosis. Pathog Dis. 2013;69:232-9 pubmed publisher..These results indicate that PE_PGRS33 is a protein with immunomodulatory activity and that protein stability and localization on the mycobacterial surface can affect these properties. ..
- Abraham P, Pathak N, Pradhan G, Sumanlatha G, Mukhopadhyay S. The N-terminal domain of Mycobacterium tuberculosis PPE17 (Rv1168c) protein plays a dominant role in inducing antibody responses in active TB patients. PLoS ONE. 2017;12:e0179965 pubmed publisher..Our data suggest that the N-terminal domain of PPE17 protein is immunodominant and could be used as a better serodiagnostic marker than the full-length PPE17 protein. ..
- Hjörleifsson J, Asgeirsson B. pH-Dependent Binding of Chloride to a Marine Alkaline Phosphatase Affects the Catalysis, Active Site Stability, and Dimer Equilibrium. Biochemistry. 2017;56:5075-5089 pubmed publisher..Taken together, the data support a model in which anions bind to some specific acceptor in the active site of VAP, resulting in great stabilization and catalytic rate enhancement, presumably through a different mechanism...
- Bernáldez V, Córdoba J, Andrade M, Alía A, Rodriguez A. Selection of reference genes to quantify relative expression of ochratoxin A-related genes by Penicillium nordicum in dry-cured ham. Food Microbiol. 2017;68:104-111 pubmed publisher..Therefore, the two RT-qPCR methods for the analysis of the relative expression of the otapks and otanps genes have been properly validated and can be used as control tools to avoid or minimise the presence of OTA in ham. ..
- Guo J, Zheng Z, Chen C, Lu X, Zhang Y, Zheng B. Enhanced Production of ?-Carrageenase and ?-Carrageenan Oligosaccharides through Immobilization of Thalassospira sp. Fjfst-332 with Magnetic Fe3O4-Chitosan Microspheres. J Agric Food Chem. 2017;65:7934-7943 pubmed publisher..Overall, this Fe3O4-chitosan-TF-332 microsphere has the potential to become a stable and reusable platform for large-scale production of ?-carrageenan oligosaccharides. ..
- Niehaus T, ElBadawi Sidhu M, De Crecy Lagard V, Fiehn O, Hanson A. Discovery of a widespread prokaryotic 5-oxoprolinase that was hiding in plain sight. J Biol Chem. 2017;292:16360-16367 pubmed publisher..Furthermore, it illustrates how easily metabolite damage and damage-control systems can be overlooked, even for central metabolites in model organisms. ..
- Blank P, Barrow G, Chou W, Duan L, Cane D, Christianson D. Substitution of Aromatic Residues with Polar Residues in the Active Site Pocket of epi-Isozizaene Synthase Leads to the Generation of New Cyclic Sesquiterpenes. Biochemistry. 2017;56:5798-5811 pubmed publisher..Thus, more radical nonpolar-polar amino acid substitutions should be considered when terpenoid cyclase active sites are remolded by mutagenesis with the goal of exploring and expanding product chemodiversity...
- Wang X, Chen X, Li Y, Xiao T, Jiang Y, Li M, et al. [Identification and evaluation of T cell epitopes of Rv0585c from Mycobacterium tuberculosis]. Zhonghua Liu Xing Bing Xue Za Zhi. 2017;38:665-669 pubmed publisher..96%????????????p10110??????????????????ifn-??il-2?il-4?il-10?p10112??????????????????ifn-??il-2?il-10???????????????????p<0.001?? ??? rv0585c????t?????????????????????????????????????????????????????????????????. ..
- McVey A, Medarametla P, Chee X, Bartlett S, Poso A, Spring D, et al. Structural and Functional Characterization of Malate Synthase G from Opportunistic Pathogen Pseudomonas aeruginosa. Biochemistry. 2017;56:5539-5549 pubmed publisher..Our data reveal two promising binding pockets in malate synthase G that may be exploited for drug design...
- Krefft D, Papkov A, Zylicz Stachula A, Skowron P. Thermostable proteins bioprocesses: The activity of restriction endonuclease-methyltransferase from Thermus thermophilus (RM.TthHB27I) cloned in Escherichia coli is critically affected by the codon composition of the synthetic gene. PLoS ONE. 2017;12:e0186633 pubmed publisher..The availability of active RM.TthHB27I is of practical importance in molecular biotechnology, extending the palette of available REase specificities...
- Abil Z, Ellefson J, Gollihar J, Watkins E, Ellington A. Compartmentalized partnered replication for the directed evolution of genetic parts and circuits. Nat Protoc. 2017;12:2493-2512 pubmed publisher..A single round of CPR should take ?3-5 d, whereas a whole directed evolution can be performed in 3-10 rounds, depending on selection efficiency...
- Ouedraogo D, Ball J, Iyer A, Reis R, Vodovoz M, Gadda G. Amine oxidation by d-arginine dehydrogenase in Pseudomonas aeruginosa. Arch Biochem Biophys. 2017;632:192-201 pubmed publisher..As shown by a combination of crystallography, kinetic and computational data, the shape and flexibility of loop L1 in the active site of PaDADH are important for substrate capture and broad substrate specificity. ..
- Khan M, Bhaskar A, Upadhyay S, Kumari P, Rajmani R, Jain P, et al. Protein kinase G confers survival advantage to Mycobacterium tuberculosis during latency-like conditions. J Biol Chem. 2017;292:16093-16108 pubmed publisher..In conclusion, we propose that PknG probably acts as a modulator of latency-associated signals. ..
- Kawalek A, Glabski K, Bartosik A, Fogtman A, Jagura Burdzy G. Increased ParB level affects expression of stress response, adaptation and virulence operons and potentiates repression of promoters adjacent to the high affinity binding sites parS3 and parS4 in Pseudomonas aeruginosa. PLoS ONE. 2017;12:e0181726 pubmed publisher..Overall, our data support the role of partitioning protein ParB as a transcriptional regulator in Pseudomonas aeruginosa. ..
- Jain R, Sliusarenko O, Kazmierczak B. Interaction of the cyclic-di-GMP binding protein FimX and the Type 4 pilus assembly ATPase promotes pilus assembly. PLoS Pathog. 2017;13:e1006594 pubmed publisher..As P. aeruginosa PilB is not itself a high-affinity c-di-GMP receptor, unlike many other assembly ATPases, FimX may play a key role in coupling T4P mediated motility and adhesion to levels of this second messenger. ..
- Rahlwes K, Ha S, Motooka D, Mayfield J, Baumoel L, Strickland J, et al. The cell envelope-associated phospholipid-binding protein LmeA is required for mannan polymerization in mycobacteria. J Biol Chem. 2017;292:17407-17417 pubmed publisher..LmeA is widespread throughout the Corynebacteriales; therefore, we concluded that LmeA is an evolutionarily conserved cell-envelope protein critical for controlling the mannan chain length of lipomannan/lipoarabinomannan. ..
- Slavin Y, Asnis J, Hafeli U, Bach H. Metal nanoparticles: understanding the mechanisms behind antibacterial activity. J Nanobiotechnology. 2017;15:65 pubmed publisher..Finally, a comprehensive analysis of the effects of NPs on the regulation of genes and proteins (transcriptomic and proteomic) profiles is discussed...
- Kim A, Ahn K, Kim H, Seo H, Kum K, Yun C, et al. Streptococcus gordonii lipoproteins induce IL-8 in human periodontal ligament cells. Mol Immunol. 2017;91:218-224 pubmed publisher..gordonii for the induction of IL-8 production in human PDL cells through TLR2 activation. Therefore, lipoproteins potentially contribute to inflammatory apical periodontitis...
- Geeraerts Z, Rodgers K, Dubois J, Lukat Rodgers G. Active Sites of O2-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron-Ligand Vibrational Correlations. Biochemistry. 2017;56:4509-4524 pubmed publisher..Moreover, they provide general insight into the structural basis of reactivity toward substrates in heme-dependent enzymes and their mechanistic intermediates, especially those containing the ferryl moiety...
- Toliusis P, Zaremba M, Silanskas A, Szczelkun M, Siksnys V. CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction endonucleases. Nucleic Acids Res. 2017;45:8435-8447 pubmed publisher..Our results are consistent with a mechanism of CglI action that is distinct from that of other ATP-dependent restriction-modification enzymes. ..
- Tamai E, Sekiya H, Maki J, Nariya H, Yoshida H, Kamitori S. X-ray structure of Clostridium perfringens sortase B cysteine transpeptidase. Biochem Biophys Res Commun. 2017;493:1267-1272 pubmed publisher..The movement of Cys232 between the two forms may help His136 deprotonate Cys232 to be activated as a thiolate, which may the catalytic Cys-activated mechanism for Srts...
- Qasem Abdullah H, Perach M, Livnat Levanon N, Lewinson O. ATP binding and hydrolysis disrupt the high-affinity interaction between the heme ABC transporter HmuUV and its cognate substrate-binding protein. J Biol Chem. 2017;292:14617-14624 pubmed publisher..Subsequent ATP hydrolysis leads to substrate delivery to the cytoplasm, release of the SBP, and resetting of the system. We propose that other Type II ABC transporters likely share the fundamentals of this mechanism. ..
- Zhao X, Li P, An K, Jia X, Cheng Y, Jia T. Chlamydia pneumoniae inclusion membrane protein Cpn0147 interacts with host protein CREB3. PLoS ONE. 2017;12:e0185593 pubmed publisher..The above observations suggest that CREB3 may directly bind to the cytoplasmic domain of Cpn0147 to mediate the interactions of chlamydial inclusions with host cell endoplasmic reticulum. ..
- Espinosa Cueto P, Magallanes Puebla A, Castellanos C, Mancilla R. Dendritic cells that phagocytose apoptotic macrophages loaded with mycobacterial antigens activate CD8 T cells via cross-presentation. PLoS ONE. 2017;12:e0182126 pubmed publisher..Taken together, these findings support a model in which phagocytosis of whole apoptotic cells carrying mycobacterial antigens promotes a potentially protective immune response. ..
- Sedlyarova N, Rescheneder P, Magán A, Popitsch N, Rziha N, Bilusic I, et al. Natural RNA Polymerase Aptamers Regulate Transcription in E. coli. Mol Cell. 2017;67:30-43.e6 pubmed publisher..iRAPs encoded in the antisense strand also promote gene expression by reducing transcriptional interference. In essence, our work uncovers a broad class of cis-acting RNA signals that globally control bacterial transcription. ..
- Govindarajan S, Amster Choder O. The bacterial Sec system is required for the organization and function of the MreB cytoskeleton. PLoS Genet. 2017;13:e1007017 pubmed publisher..Taken together, our data reveal that the secretion system plays an important role in determining the organization and functioning of the cytoskeletal system in bacteria. ..
- Wang J, Ren X, Wang R, Su J, Wang F. Structural Characteristics and Function of a New Kind of Thermostable Trehalose Synthase from Thermobaculum terrenum. J Agric Food Chem. 2017;65:7726-7735 pubmed publisher..The detailed thermophilic enzyme structure provided herein may provide guidance for further protein engineering in the design of stabilized enzymes. ..
- Kern B, Porsch E, St Geme J. Defining the Mechanical Determinants of Kingella kingae Adherence to Host Cells. J Bacteriol. 2017;199: pubmed publisher..This work provides new insight into the interplay of T4P, a nonpilus adhesin, and a capsule and their effects on bacterial adherence to host cells. ..
- Mi W, Li Y, Yoon S, Ernst R, Walz T, Liao M. Structural basis of MsbA-mediated lipopolysaccharide transport. Nature. 2017;549:233-237 pubmed publisher..Our study uncovers the structural basis for LPS recognition, delineates the conformational transitions of MsbA to flip LPS, and paves the way for structural characterization of other lipid flippases. ..
- Tada T, Tsuchiya M, Shimada K, Nga T, Thu L, Phu T, et al. Dissemination of Carbapenem-resistant Klebsiella pneumoniae clinical isolates with various combinations of Carbapenemases (KPC-2, NDM-1, NDM-4, and OXA-48) and 16S rRNA Methylases (RmtB and RmtC) in Vietnam. BMC Infect Dis. 2017;17:467 pubmed publisher..This is the first report of KPC-2, NDM-4 and OXA-48 producers in a medical setting in Vietnam. ..
- Seng R, Kitti T, Thummeepak R, Kongthai P, Leungtongkam U, Wannalerdsakun S, et al. Biofilm formation of methicillin-resistant coagulase negative staphylococci (MR-CoNS) isolated from community and hospital environments. PLoS ONE. 2017;12:e0184172 pubmed publisher..The high prevalence of biofilm producing MR-CoNS strains demonstrated in this study indicates the persisting ability in environments, and is useful in developing prevention strategies countering the spread of MR-CoNS...
- Chakravarty S, Melton C, Bailin A, Yahr T, Anderson G. Pseudomonas aeruginosa Magnesium Transporter MgtE Inhibits Type III Secretion System Gene Expression by Stimulating rsmYZ Transcription. J Bacteriol. 2017;199: pubmed publisher..aeruginosa In this study, we describe the mechanism of MgtE-dependent inhibition of the T3SS. Our report also illustrates how MgtE might respond to environmental cues, such as magnesium levels, to fine-tune T3SS gene expression. ..