Publications

expression and characterization of a novel glycerophosphodiester phosphodiesterase from pyrococcus furiosus dsm 3638 that possesses lysophospholipase d activity.	glycerophosphodiester phosphodiesterases (gdpd) are enzymes which degrade various glycerophosphodiesters to produce glycerol-3-phosphate and the corresponding alcohol moiety. apart from this, a very interesting finding is that this enzyme could be used in the degradation of toxic organophosphorus esters, which has resulted in much attention on the biochemical and application research of gdpds. in the present study, a novel gdpd from pyrococcus furiosus dsm 3638 (pfgdpd) was successfully expresse ...	2016	27248999
elongation factor tu prevents misediting of gly-trna(gly) caused by the design behind the chiral proofreading site of d-aminoacyl-trna deacylase.	d-aminoacyl-trna deacylase (dtd) removes d-amino acids mischarged on trnas and is thus implicated in enforcing homochirality in proteins. previously, we proposed that selective capture of d-aminoacyl-trna by dtd's invariant, cross-subunit gly-cispro motif forms the mechanistic basis for its enantioselectivity. we now show, using nuclear magnetic resonance (nmr) spectroscopy-based binding studies followed by biochemical assays with both bacterial and eukaryotic systems, that dtd effectively mised ...	2016	27224426
abundance and temperature dependency of protein-protein interaction revealed by interface structure analysis and stability evolution.	protein complexes are major forms of protein-protein interactions and implement essential biological functions. the subunit interface in a protein complex is related to its thermostability. though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. in the present work, we studied this relationship and found a positive correlation in thermophiles ...	2016	27220911
essential structural elements in trna(pro) for ef-p-mediated alleviation of translation stalling.	the ribosome stalls on translation of polyproline sequences due to inefficient peptide bond formation between consecutive prolines. the translation factor ef-p is able to alleviate this stalling by accelerating pro-pro formation. however, the mechanism by which ef-p recognizes the stalled complexes and accelerates peptide bond formation is not known. here, we use genetic code reprogramming through a flexible in-vitro translation (fit) system to investigate how mutations in trna(pro) affect ef-p ...	2016	27216360
crystal structure of glutamate-1-semialdehyde-2,1-aminomutase from arabidopsis thaliana.	glutamate-1-semialdehyde-2,1-aminomutase (gsam) catalyzes the isomerization of glutamate-1-semialdehyde (gsa) to 5-aminolevulinate (ala) and is distributed in archaea, most bacteria and plants. although structures of gsam from archaea and bacteria have been resolved, a gsam structure from a higher plant is not available, preventing further structure-function analysis. here, the structure of gsam from arabidopsis thaliana (atgsa1) obtained by x-ray crystallography is reported at 1.25 å resolution ...	2016	27303897
the pilin n-terminal domain maintains neisseria gonorrhoeae transformation competence during pilus phase variation.	the obligate human pathogen neisseria gonorrhoeae is the sole aetiologic agent of the sexually transmitted infection, gonorrhea. required for gonococcal infection, type iv pili (tfp) mediate many functions including adherence, twitching motility, defense against neutrophil killing, and natural transformation. critical for immune escape, the gonococcal tfp undergoes antigenic variation, a recombination event at the pile locus that varies the surface exposed residues of the major pilus subunit pil ...	2016	27213957
wake me when it's over - bacterial toxin-antitoxin proteins and induced dormancy.	toxin-antitoxin systems are encoded by bacteria and archaea to enable an immediate response to environmental stresses, including antibiotics and the host immune response. during normal conditions, the antitoxin components prevent toxins from interfering with metabolism and arresting growth; however, toxin activation enables microbes to remain dormant through unfavorable conditions that might continue over millions of years. intense investigations have revealed a multitude of mechanisms for both ...	2016	27216598
structure of human cdc45 and implications for cmg helicase function.	cell division cycle protein 45 (cdc45) is required for dna synthesis during genome duplication, as a component of the cdc45-mcm-gins (cmg) helicase. despite its essential biological function, its biochemical role in dna replication has remained elusive. here we report the 2.1-å crystal structure of human cdc45, which confirms its evolutionary link with the bacterial recj nuclease and reveals several unexpected features that underpin its function in eukaryotic dna replication. these include a lon ...	2016	27189187
anatomy of risc: how do small rnas and chaperones activate argonaute proteins?	rna silencing is a eukaryote-specific phenomenon in which micrornas and small interfering rnas degrade messenger rnas containing a complementary sequence. to this end, these small rnas need to be loaded onto an argonaute protein (ago protein) to form the effector complex referred to as rna-induced silencing complex (risc). risc assembly undergoes multiple and sequential steps with the aid of hsc70/hsp90 chaperone machinery. the molecular mechanisms for this assembly process remain unclear, despi ...	2016	27184117
silica-induced protein (sip) in thermophilic bacterium thermus thermophilus responds to low iron availability.	thermus thermophilus hb8 expresses silica-induced protein (sip) when cultured in medium containing supersaturated silicic acids. using genomic information, sip was identified as a fe(3+)-binding abc transporter. detection of a 1-kb hybridized band in northern analysis revealed that sip transcription is monocistronic and that sip has its own terminator and promoter. the sequence of the sip promoter showed homology with that of the σ(a)-dependent promoter, which is known as a housekeeping promoter ...	2016	26994077
cyclic amp receptor protein acts as a transcription regulator in response to stresses in deinococcus radiodurans.	the cyclic amp receptor protein family of transcription factors regulates various metabolic pathways in bacteria, and also play roles in response to environmental changes. here, we identify four homologs of the crp family in deinococcus radiodurans, one of which tolerates extremely high levels of oxidative stress and dna-damaging reagents. transcriptional levels of crp were increased under hydrogen peroxide (h2o2) treatment during the stationary growth phase, indicating that crps function in res ...	2016	27182600
global quantitative proteomics reveal up-regulation of endoplasmic reticulum stress response proteins upon depletion of eif5a in hela cells.	the eukaryotic translation factor, eif5a, is a translation factor essential for protein synthesis, cell growth and animal development. by use of a adenoviral eif5a shrna, we have achieved an effective depletion of eif5a in hela cells and undertook in vivo comprehensive proteomic analyses to examine the effects of eif5a depletion on the total proteome and to identify cellular pathways influenced by eif5a. the proteome of hela cells transduced with eif5a shrna was compared with that of scramble sh ...	2016	27180817
the diversity of ribonuclease p: protein and rna catalysts with analogous biological functions.	ribonuclease p (rnase p) is an essential endonuclease responsible for catalyzing 5' end maturation in precursor transfer rnas. since its discovery in the 1970s, rnase p enzymes have been identified and studied throughout the three domains of life. interestingly, rnase p is either rna-based, with a catalytic rna subunit, or a protein-only (prorp) enzyme with differential evolutionary distribution. the available structural data, including the active site data, provides insight into catalysis and s ...	2016	27187488
the crispr rna-guided surveillance complex in escherichia coli accommodates extended rna spacers.	bacteria and archaea acquire resistance to foreign genetic elements by integrating fragments of foreign dna into crispr (clustered regularly interspaced short palindromic repeats) loci. in escherichia coli, crispr-derived rnas (crrnas) assemble with cas proteins into a multi-subunit surveillance complex called cascade (crispr-associated complex for antiviral defense). cascade recognizes dna targets via protein-mediated recognition of a protospacer adjacent motif and complementary base pairing be ...	2016	27174938
a water-forming nadh oxidase regulates metabolism in anaerobic fermentation.	water-forming nadh oxidase can oxidize cytosolic nadh to nad(+), thus relieving cytosolic nadh accumulation in saccharomyces cerevisiae. previous studies of the enzyme were conducted under aerobic conditions, as o2 is the recognized electron acceptor of the enzyme. in order to extend its use in industrial production and to study its effect on anaerobes, the effects of overexpression of this oxidase in s. cerevisiae by4741 and clostridium acetobutylicum 428 (cac-428) under anaerobic conditions we ...	2016	27175216
zinc coordination is essential for the function and activity of the type ii secretion atpase epse.	the type ii secretion system eps in vibrio cholerae promotes the extracellular transport of cholera toxin and several hydrolytic enzymes and is a major virulence system in many gram-negative pathogens which is structurally related to the type iv pilus system. the cytoplasmic atpase epse provides the energy for exoprotein secretion through atp hydrolysis. epse contains a unique metal-binding domain that coordinates zinc through a tetracysteine motif (cxxcx29 cxxc), which is also present in type i ...	2016	27168165
ribosome-dependent activation of stringent control.	in order to survive, bacteria continually sense, and respond to, environmental fluctuations. stringent control represents a key bacterial stress response to nutrient starvation that leads to rapid and comprehensive reprogramming of metabolic and transcriptional patterns. in general, transcription of genes for growth and proliferation is downregulated, while those important for survival and virulence are upregulated. amino acid starvation is sensed by depletion of the aminoacylated trna pools, an ...	2016	27279228
the comparatively proteomic analysis in response to cold stress in cassava plantlets.	cassava (manihot esculenta crantz) is a tropical root crop and sensitive to low temperature. however, it is poorly to know how cassava can modify its metabolism and growth to adapt to cold stress. an investigation aimed at a better understanding of cold-tolerant mechanism of cassava plantlets was carried out with the approaches of physiology and proteomics in the present study. the principal component analysis of seven physiological characteristics showed that electrolyte leakage (el), chlorophy ...	2016	27881899
bioprospecting sponge-associated microbes for antimicrobial compounds.	sponges are the most prolific marine organisms with respect to their arsenal of bioactive compounds including antimicrobials. however, the majority of these substances are probably not produced by the sponge itself, but rather by bacteria or fungi that are associated with their host. this review for the first time provides a comprehensive overview of antimicrobial compounds that are known to be produced by sponge-associated microbes. we discuss the current state-of-the-art by grouping the bioact ...	2016	27144573
characterization of the atp-dependent lon-like protease in methanobrevibacter smithii.	the lon protease is highly evolutionarily conserved. however, little is known about lon in the context of gut microbial communities. a gene encoding a lon-like protease (lon-like-ms) was identified and characterized from methanobrevibacter smithii, the predominant archaeon in the human gut ecosystem. phylogenetic and sequence analyses showed that lon-like-ms and its homologs are newly identified members of the lon family. a recombinant form of the enzyme was purified by affinity chromatography, ...	2016	27239160
a decade of biochemical and structural studies of the dna repair machinery of deinococcus radiodurans: major findings, functional and mechanistic insight and challenges.	the deinococcus radiodurans bacterium is extremely resistant to ionising radiation and desiccation and can withstand a 200-fold higher radiation dose than most other bacteria with no loss of viability. the mechanisms behind this extreme resistance are not fully understood, but it is clear that several factors contribute to this phenotype. efficient scavenging of reactive oxygen species and repair of damaged dna are two of these. in this review, we summarise the results from a decade of structura ...	2016	27924191
life without complex i: proteome analyses of an arabidopsis mutant lacking the mitochondrial nadh dehydrogenase complex.	the mitochondrial nadh dehydrogenase complex (complex i) is of particular importance for the respiratory chain in mitochondria. it is the major electron entry site for the mitochondrial electron transport chain (metc) and therefore of great significance for mitochondrial atp generation. we recently described an arabidopsis thaliana double-mutant lacking the genes encoding the carbonic anhydrases ca1 and ca2, which both form part of a plant-specific 'carbonic anhydrase domain' of mitochondrial co ...	2016	27122571
crystal structures of apo and liganded 4-oxalocrotonate decarboxylase uncover a structural basis for the metal-assisted decarboxylation of a vinylogous β-keto acid.	the enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. in a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria pseudomonas putida g7. in this organism, the 83 kb nah7 plasmid carries several genes involved in this biotransformation process. one enzyme in this route, nahk, ...	2016	27082660
engineering a d-lactate dehydrogenase that can super-efficiently utilize nadph and nadh as cofactors.	engineering the cofactor specificity of a natural enzyme often results in a significant decrease in its activity on original cofactor. here we report that a nadh-dependent dehydrogenase (d-ldh) from lactobacillus delbrueckii 11842 can be rationally engineered to efficiently use both nadh and nadph as cofactors. point mutations on three amino acids (d176s, i177r, f178t) predicted by computational analysis resulted in a modified enzyme designated as d-ldh. the kcat/km of the purified d-ldh on na ...	2016	27109778
a polymorphism in leus confers reduced susceptibility to gsk2251052 in a clinical isolate of staphylococcus aureus.	gsk2251052 is a broad-spectrum antibacterial inhibitor of leucyl trna-synthetase (leurs) that has been evaluated in phase ii clinical trials. here, we report the identification of a clinical isolate of staphylococcus aureus that exhibits reduced susceptibility to gsk2251052 without prior exposure to the compound and demonstrate that this phenotype is attributable to a single amino acid polymorphism (p329) within the editing domain of leurs.	2016	26976861
functional characterization of the subunits n, h, j, and o of the nad(p)h dehydrogenase complexes in synechocystis sp. strain pcc 6803.	the cyanobacterial nad(p)h dehydrogenase (ndh-1) complexes play crucial roles in variety of bioenergetic reactions such as respiration, co2 uptake, and cyclic electron transport around psi. recently, substantial progress has been made in identifying the composition of subunits of ndh-1 complexes. however, the localization and the physiological roles of several subunits in cyanobacteria are not fully understood. here, by constructing fully segregated ndhn, ndho, ndhh, and ndhj null mutants in syn ...	2016	27208236
nucleoside modifications in the regulation of gene expression: focus on trna.	both, dna and rna nucleoside modifications contribute to the complex multi-level regulation of gene expression. modified bases in trnas modulate protein translation rates in a highly dynamic manner. synonymous codons, which differ by the third nucleoside in the triplet but code for the same amino acid, may be utilized at different rates according to codon-anticodon affinity. nucleoside modifications in the trna anticodon loop can favor the interaction with selected codons by stabilizing specific ...	2016	27094388
the ancient evolutionary history of polyomaviruses.	polyomaviruses are a family of dna tumor viruses that are known to infect mammals and birds. to investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billi ...	2016	27093155
elongation factor 4 remodels the a-site trna on the ribosome.	during translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. many of those factors are guanosine triphosphatases (gtpases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (gtp) to promote conformational changes. despite numerous studies, the function of elongation factor 4 (ef-4/lepa), a highly conserved translational gtpase, has remained elusive. here, we present the crystal structure at 2.6-å resolution of the thermus thermophilus 7 ...	2016	27092003
evolutionary relationships between heme-binding ferredoxin α + β barrels.	the α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. the barrel architecture of these proteins is formed by either homo-/hetero-dimerization or duplication and fusion of ferredoxin-like domains. several members of this superfamily bind heme in order to carry out their functions.	2016	27089923
insights into rna binding by the anticancer drug cisplatin from the crystal structure of cisplatin-modified ribosome.	cisplatin is a widely prescribed anticancer drug, which triggers cell death by covalent binding to a broad range of biological molecules. among cisplatin targets, cellular rnas remain the most poorly characterized molecules. although cisplatin was shown to inactivate essential rnas, including ribosomal, spliceosomal and telomeric rnas, cisplatin binding sites in most rna molecules are unknown, and therefore it remains challenging to study how modifications of rna by cisplatin contributes to its ...	2016	27079977
structural basis for dna 5´-end resection by recj.	the resection of dna strand with a 5´ end at double-strand breaks is an essential step in recombinational dna repair. recj, a member of dhh family proteins, is the only 5´ nuclease involved in the recf recombination pathway. here, we report the crystal structures of deinococcus radiodurans recj in complex with deoxythymidine monophosphate (dtmp), ssdna, the c-terminal region of single-stranded dna-binding protein (ssb-ct) and a mechanistic insight into the recf pathway. a terminal 5´-phosphate-b ...	2016	27058167
inhibition of translation initiation complex formation by ge81112 unravels a 16s rrna structural switch involved in p-site decoding.	in prokaryotic systems, the initiation phase of protein synthesis is governed by the presence of initiation factors that guide the transition of the small ribosomal subunit (30s) from an unlocked preinitiation complex (30s preic) to a locked initiation complex (30sic) upon the formation of a correct codon-anticodon interaction in the peptidyl (p) site. biochemical and structural characterization of ge81112, a translational inhibitor specific for the initiation phase, indicates that the main mech ...	2016	27071098
escherichia coli dnae polymerase couples pyrophosphatase activity to dna replication.	dna polymerases generate pyrophosphate every time they catalyze a step of dna elongation. this elongation reaction is generally believed as thermodynamically favoured by the hydrolysis of pyrophosphate, catalyzed by inorganic pyrophosphatases. however, the specific action of inorganic pyrophosphatases coupled to dna replication in vivo was never demonstrated. here we show that the polymerase-histidinol-phosphatase (php) domain of escherichia coli dna polymerase iii α subunit features pyrophospha ...	2016	27050298
unlocking the bacterial secy translocon.	the sec translocon performs protein secretion and membrane protein insertion at the plasma membrane of bacteria and archaea (secyeg/β), and the endoplasmic reticular membrane of eukaryotes (sec61). despite numerous structures of the complex, the mechanism underlying translocation of pre-proteins, driven by the atpase seca in bacteria, remains unresolved. here we present a series of biochemical and computational analyses exploring the consequences of signal sequence binding to secyeg. the data de ...	2016	26973090
a bacterial argonaute with noncanonical guide rna specificity.	eukaryotic argonaute proteins induce gene silencing by small rna-guided recognition and cleavage of mrna targets. although structural similarities between human and prokaryotic argonautes are consistent with shared mechanistic properties, sequence and structure-based alignments suggested that argonautes encoded within crispr-cas [clustered regularly interspaced short palindromic repeats (crispr)-associated] bacterial immunity operons have divergent activities. we show here that the crispr-associ ...	2016	27035975
a critical base pair in k-turns determines the conformational class adopted, and correlates with biological function.	k-turns are commonly-occurring motifs that introduce sharp kinks into duplex rna, thereby facilitating tertiary contacts. both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called n3 and n1, that differ in the pattern of hydrogen bonding in the core. we show here that this is determined by the basepair adjacent to the critical g•a pairs. we determined crystal structures of a series of kt-7 variants in which this 3b,3 ...	2016	27016741
trna core hypothesis for the transition from the rna world to the ribonucleoprotein world.	herein we present the trna core hypothesis, which emphasizes the central role of trnas molecules in the origin and evolution of fundamental biological processes. trnas gave origin to the first genes (mrna) and the peptidyl transferase center (rrna), proto-trnas were at the core of a proto-translation system, and the anticodon and operational codes then arose in trnas molecules. metabolic pathways emerged from evolutionary pressures of the decoding systems. the transitions from the rna world to t ...	2016	27023615
targeting antibiotic resistance.	finding strategies against the development of antibiotic resistance is a major global challenge for the life sciences community and for public health. the past decades have seen a dramatic worldwide increase in human-pathogenic bacteria that are resistant to one or multiple antibiotics. more and more infections caused by resistant microorganisms fail to respond to conventional treatment, and in some cases, even last-resort antibiotics have lost their power. in addition, industry pipelines for th ...	2016	27000559
mechanism of fusidic acid inhibition of rrf- and ef-g-dependent splitting of the bacterial post-termination ribosome.	the antibiotic drug fusidic acid (fa) is commonly used in the clinic against gram-positive bacterial infections. fa targets ribosome-bound elongation factor g (ef-g), a translational gtpase that accelerates both messenger rna (mrna) translocation and ribosome recycling. how fa inhibits translocation was recently clarified, but fa inhibition of ribosome recycling by ef-g and ribosome recycling factor (rrf) has remained obscure. here we use fast kinetics techniques to estimate mean times of riboso ...	2016	27001509
functional determinants of metal ion transport and selectivity in paralogous cation diffusion facilitator transporters czcd and mnte in streptococcus pneumoniae.	cation diffusion facilitators (cdfs) are a large family of divalent metal transporters that collectively possess broad metal specificity and contribute to intracellular metal homeostasis and virulence in bacterial pathogens. streptococcus pneumoniae expresses two homologous cdf efflux transporters, mnte and czcd. cells lacking mnte or czcd are sensitive to manganese (mn) or zinc (zn) toxicity, respectively, and specifically accumulate mn or zn, respectively, thus suggesting that mnte selectively ...	2016	26787764
(1)h, (13)c and (15)n resonance assignments and secondary structure analysis of translation initiation factor 1 from pseudomonas aeruginosa.	pseudomonas aeruginosa is a gram-negative opportunistic pathogen and a primary cause of infection in humans. p. aeruginosa can acquire resistance against multiple groups of antimicrobial agents, including β-lactams, aminoglycosides and fluoroquinolones, and multidrug resistance is increasing in this organism which makes treatment of the infections difficult and expensive. this has led to the unmet need for discovery of new compounds distinctly different from present antimicrobials. protein synth ...	2016	26983940
insight into the flagella type iii export revealed by the complex structure of the type iii atpase and its regulator.	flii and flij form the flii6flij atpase complex of the bacterial flagellar export apparatus, a member of the type iii secretion system. the flii6flij complex is structurally similar to the α3β3γ complex of f1-atpase. the flih homodimer binds to flii to connect the atpase complex to the flagellar base, but the details are unknown. here we report the structure of the homodimer of a c-terminal fragment of flih (flihc2) in complex with flii. flihc2 shows an unusually asymmetric homodimeric structure ...	2016	26984495
from chlorite dismutase towards hemq - the role of the proximal h-bonding network in haeme binding.	chlorite dismutase (cld) and hemq are structurally and phylogenetically closely related haeme enzymes differing fundamentally in their enzymatic properties. clds are able to convert chlorite into chloride and dioxygen, whereas hemq is proposed to be involved in the haeme b synthesis of gram-positive bacteria. a striking difference between these protein families concerns the proximal haeme cavity architecture. the pronounced h-bonding network in cld, which includes the proximal ligand histidine a ...	2016	26858461
stability of ensemble models predicts productivity of enzymatic systems.	stability in a metabolic system may not be obtained if incorrect amounts of enzymes are used. without stability, some metabolites may accumulate or deplete leading to the irreversible loss of the desired operating point. even if initial enzyme amounts achieve a stable steady state, changes in enzyme amount due to stochastic variations or environmental changes may move the system to the unstable region and lose the steady-state or quasi-steady-state flux. this situation is distinct from the pheno ...	2016	26963521
crystal structure of a substrate-engaged secy protein-translocation channel.	hydrophobic signal sequences target secretory polypeptides to a protein-conducting channel formed by a heterotrimeric membrane protein complex, the prokaryotic secy or eukaryotic sec61 complex. how signal sequences are recognized is poorly understood, particularly because they are diverse in sequence and length. structures of the inactive channel show that the largest subunit, secy or sec61α, consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membr ...	2016	26950603
structural dynamics of human argonaute2 and its interaction with sirnas designed to target mutant tdp43.	the human argonaute2 protein (ago2) is a key player in rna interference pathway and small rna recognition by ago2 is the crucial step in sirna mediated gene silencing mechanism. the present study highlights the structural and functional dynamics of human ago2 and the interaction mechanism of ago2 with a set of seven sirnas for the first time. the human ago2 protein adopts two conformations such as "open" and "close" during the simulation of 25 ns. one of the domains named as paz, which is respon ...	2016	27110240
genomic and transcriptomic analysis of the streptomycin-dependent mycobacterium tuberculosis strain 18b.	the ability of mycobacterium tuberculosis to establish a latent infection (ltbi) in humans confounds the treatment of tuberculosis. consequently, there is a need to discover new therapeutic agents that can kill m. tuberculosis both during active disease and ltbi. the streptomycin-dependent strain of m. tuberculosis, 18b, provides a useful tool for this purpose since upon removal of streptomycin (str) it enters a non-replicating state that mimics latency both in vitro and in animal models.	2016	26944551
structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association.	throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trgtpase). although the structural basis for trgtpase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trgtpase, initiation factor 2 (if2), complexed with the ribosome, remains elusive. we determine t ...	2016	26973877
structural basis for the endoribonuclease activity of the type iii-a crispr-associated protein csm6.	prokaryotic crispr-cas systems provide an rna-guided mechanism for genome defense against mobile genetic elements such as viruses and plasmids. in type iii-a crispr-cas systems, the rna-guided multisubunit csm effector complex targets both single-stranded rnas and double-stranded dnas. in addition to the csm complex, efficient anti-plasmid immunity mediated by type iii-a systems also requires the crispr-associated protein csm6. here we report the crystal structure of csm6 from thermus thermophil ...	2016	26763118
impact of different target sequences on type iii crispr-cas immunity.	clustered regularly interspaced short palindromic repeat (crispr) loci encode an adaptive immune system of prokaryotes. within these loci, sequences intercalated between repeats known as "spacers" specify the targets of crispr immunity. the majority of spacers match sequences present in phages and plasmids; however, it is not known whether there are differences in the immunity provided against these diverse invaders. we studied this issue using the staphylococcus epidermidis crispr system, which ...	2016	26755632
cooperation between two periplasmic copper chaperones is required for full activity of the cbb3 -type cytochrome c oxidase and copper homeostasis in rhodobacter capsulatus.	copper (cu) is an essential micronutrient that functions as a cofactor in several important enzymes, such as respiratory heme-copper oxygen reductases. yet, cu is also toxic and therefore cells engage a highly coordinated cu uptake and delivery system to prevent the accumulation of toxic cu concentrations. in this study, we analyzed cu delivery to the cbb3 -type cytochrome c oxidase (cbb3 -cox) of rhodobacter capsulatus. we identified the pcua c-like periplasmic chaperone pcca and analyzed its c ...	2016	26718481
the kink turn, a key architectural element in rna structure.	kink turns (k-turns) are widespread structural elements that introduce an axial bend into duplex rna with an included angle of 50°. these mediate key tertiary interactions and bind specific proteins including members of the l7ae family. the standard k-turn comprises a three-nucleotide bulge followed by g·a and a·g pairs. the rna kinks by an association of the two minor grooves, stabilized by the formation of a number of key cross-strand hydrogen bonds mostly involving the adenine bases of the g· ...	2016	26522935
naturally occurring isoleucyl-trna synthetase without trna-dependent pre-transfer editing.	isoleucyl-trna synthetase (ilers) is unusual among aminoacyl-trna synthetases in having a trna-dependent pre-transfer editing activity. alongside the typical bacterial ilers (such as escherichia coli ilers), some bacteria also have the enzymes (eukaryote-like) that cluster with eukaryotic ilerss and exhibit low sensitivity to the antibiotic mupirocin. our phylogenetic analysis suggests that the iles1 and iles2 genes of contemporary bacteria are the descendants of genes that might have arisen by ...	2016	26921320
in-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth.	precise protein structure determination provides significant information on life science research, although high-quality crystals are not easily obtained. we developed a system for producing high-quality protein crystals with high throughput. using this system, gravity-controlled crystallization are made possible by a magnetic microgravity environment. in addition, in-situ and real-time observation and time-lapse imaging of crystal growth are feasible for over 200 solution samples independently. ...	2016	26916802
atp binding by the p-loop ntpase osychf1 (an unconventional g protein) contributes to biotic but not abiotic stress responses.	g proteins are involved in almost all aspects of the cellular regulatory pathways through their ability to bind and hydrolyze gtp. the ychf subfamily, interestingly, possesses the unique ability to bind both atp and gtp, and is possibly an ancestral form of g proteins based on phylogenetic studies and is present in all kingdoms of life. however, the biological significance of such a relaxed ligand specificity has long eluded researchers. here, we have elucidated the different conformational chan ...	2016	26912459
systematic evolution and study of uagn decoding trnas in a genomically recoded bacteria.	we report the first systematic evolution and study of trna variants that are able to read a set of uagn (n = a, g, u, c) codons in a genomically recoded e. coli strain that lacks any endogenous in-frame uagn sequences and release factor 1. through randomizing bases in anticodon stem-loop followed by a functional selection, we identified trna mutants with significantly improved uagn decoding efficiency, which will augment the current efforts on genetic code expansion through quadruplet decoding. ...	2016	26906548
substrate recognition and cleavage-site selection by a single-subunit protein-only rnase p.	rnase p is the enzyme that removes 5' extensions from trna precursors. with its diversity of enzyme forms-either protein- or rna-based, ranging from single polypeptides to multi-subunit ribonucleoproteins-the rnase p enzyme family represents a unique model system to compare the evolution of enzymatic mechanisms. here we present a comprehensive study of substrate recognition and cleavage-site selection by the nuclear single-subunit proteinaceous rnase p prorp3 from arabidopsis thaliana. compared ...	2016	26896801
the trade-off of availability and growth inhibition through copper for the production of copper-dependent enzymes by pichia pastoris.	copper is an essential chemical element for life as it is a part of prosthetic groups of enzymes including super oxide dismutase and cytochrome c oxidase; however, it is also toxic at high concentrations. here, we present the trade-off of copper availability and growth inhibition of a common host used for copper-dependent protein production, pichia pastoris.	2016	26897180
curing the megaplasmid ptt27 from thermus thermophilus hb27 and maintaining exogenous plasmids in the plasmid-free strain.	stepwise deletions in the only plasmid in thermus thermophilus hb27, megaplasmid ptt27, showed that two distantly located loci were important for maintenance of the plasmid. one is a minimum replicon including one gene, rept, coding a replication initiator, and the other encodes subunits of class i ribonucleotide reductase (rnr) for deoxynucleoside triphosphate (dntp) synthesis. since the initiator protein, rept, bound to direct repeats downstream from its own gene, it was speculated that a more ...	2016	26712540
aerobic and anaerobic thiosulfate oxidation by a cold-adapted, subglacial chemoautotroph.	geochemical data indicate that protons released during pyrite (fes2) oxidation are important drivers of mineral weathering in oxic and anoxic zones of many aquatic environments, including those beneath glaciers. oxidation of fes2 under oxic, circumneutral conditions proceeds through the metastable intermediate thiosulfate (s2o3 (2-)), which represents an electron donor capable of supporting microbial metabolism. subglacial meltwaters sampled from robertson glacier (rg), canada, over a seasonal m ...	2016	26712544
all the o2 consumed by thermus thermophilus cytochrome ba3 is delivered to the active site through a long, open hydrophobic tunnel with entrances within the lipid bilayer.	cytochrome ba3 is a proton-pumping heme-copper oxygen reductase from the extreme thermophile thermus thermophilus. despite the fact that the enzyme's active site is buried deep within the protein, the apparent second order rate constant for the initial binding of o2 to the active-site heme has been experimentally found to be 10(9) m(-1) s(-1) at 298 k, at or near the diffusion limit, and 2 orders of magnitude faster than for o2 binding to myoglobin. to provide quantitative and microscopic descri ...	2016	26845082
purification and characterization of glutaminase free asparaginase from enterobacter cloacae: in-vitro evaluation of cytotoxic potential against human myeloid leukemia hl-60 cells.	asparaginase is an important antileukemic agent extensively used worldwide but the intrinsic glutaminase activity of this enzymatic drug is responsible for serious life threatening side effects. hence, glutaminase free asparaginase is much needed for upgradation of therapeutic index of asparaginase therapy. in the present study, glutaminase free asparaginase produced from enterobacter cloacae was purified to apparent homogeneity. the purified enzyme was found to be homodimer of approximately 106 ...	2016	26891220
chemical control of xylem differentiation by thermospermine, xylemin, and auxin.	the xylem conducts water and minerals from the root to the shoot and provides mechanical strength to the plant body. the vascular precursor cells of the procambium differentiate to form continuous vascular strands, from which xylem and phloem cells are generated in the proper spatiotemporal pattern. procambium formation and xylem differentiation are directed by auxin. in angiosperms, thermospermine, a structural isomer of spermine, suppresses xylem differentiation by limiting auxin signalling. h ...	2016	26879262
role of protein phosphorylation in the regulation of cell cycle and dna-related processes in bacteria.	in all living organisms, the phosphorylation of proteins modulates various aspects of their functionalities. in eukaryotes, protein phosphorylation plays a key role in cell signaling, gene expression, and differentiation. protein phosphorylation is also involved in the global control of dna replication during the cell cycle, as well as in the mechanisms that cope with stress-induced replication blocks. similar to eukaryotes, bacteria use hanks-type kinases and phosphatases for signal transductio ...	2016	26909079
ribosomal small subunit domains radiate from a central core.	the domain architecture of a large rna can help explain and/or predict folding, function, biogenesis and evolution. we offer a formal and general definition of an rna domain and use that definition to experimentally characterize the rrna of the ribosomal small subunit. here the rrna comprising a domain is compact, with a self-contained system of molecular interactions. a given rrna helix or stem-loop must be allocated uniquely to a single domain. local changes such as mutations can give domain-w ...	2016	26876483
isc, a novel group of bacterial and archaeal dna transposons that encode cas9 homologs.	bacterial genomes encode numerous homologs of cas9, the effector protein of the type ii crispr-cas systems. the homology region includes the arginine-rich helix and the hnh nuclease domain that is inserted into the ruvc-like nuclease domain. these genes, however, are not linked to cas genes or crispr. here, we show that cas9 homologs represent a distinct group of nonautonomous transposons, which we denote isc (insertion sequences cas9-like). we identify many diverse families of full-length isc t ...	2016	26712934
kinetic mechanism and fidelity of nick sealing by escherichia coli nad+-dependent dna ligase (liga).	escherichia coli dna ligase (ecoliga) repairs 3'-oh/5'-po4 nicks in duplex dna via reaction of liga with nad(+) to form a covalent liga-(lysyl-nζ)-amp intermediate (step 1); transfer of amp to the nick 5'-po4 to form an appdna intermediate (step 2); and attack of the nick 3'-oh on appdna to form a 3'-5' phosphodiester (step 3). a distinctive feature of ecoliga is its stimulation by ammonium ion. here we used rapid mix-quench methods to analyze the kinetic mechanism of single-turnover nick sealin ...	2016	26857547
biofuel production based on carbohydrates from both brown and red macroalgae: recent developments in key biotechnologies.	marine macroalgae (green, red and brown macroalgae) have attracted attention as an alternative source of renewable biomass for producing both fuels and chemicals due to their high content of suitable carbohydrates and to their advantages over terrestrial biomass. however, except for green macroalgae, which contain relatively easily-fermentable glucans as their major carbohydrates, practical utilization of red and brown macroalgae has been regarded as difficult due to the major carbohydrates (alg ...	2016	26861307
markerless gene deletion with cytosine deaminase in thermus thermophilus strain hb27.	we developed a counterselectable deletion system for thermus thermophilus hb27 based on cytosine deaminase (encoded by coda) from thermaerobacter marianensis dsm 12885 and the sensitivity of t. thermophilus hb27 to the antimetabolite 5-fluorocytosine (5-fc). the deletion vector comprises the puc18 origin of replication, a thermostable kanamycin resistance marker functional in t. thermophilus hb27, and coda under the control of a constitutive putative trehalose promoter from t. thermophilus hb27. ...	2016	26655764
cytoplasmic copz-like protein and periplasmic rusticyanin and acop proteins as possible copper resistance determinants in acidithiobacillus ferrooxidans atcc 23270.	acidophilic organisms, such as acidithiobacillus ferrooxidans, possess high-level resistance to copper and other metals. a. ferrooxidans contains canonical copper resistance determinants present in other bacteria, such as copa atpases and rnd efflux pumps, but these components do not entirely explain its high metal tolerance. the aim of this study was to find other possible copper resistance determinants in this bacterium. transcriptional expression of a. ferrooxidans genes coding for a cytoplas ...	2016	26637599
interaction network of tobacco etch potyvirus nia protein with the host proteome during infection.	the genomes of plant viruses have limited coding capacity, and to complete their infectious cycles, viral factors must target, direct or indirectly, many host elements. however, the interaction networks between viruses and host factors are poorly understood. the genus potyvirus is the largest group of plus-strand rna viruses infecting plants. potyviral nuclear inclusion a (nia) plays many roles during infection. nia is a polyprotein consisting of two domains, viral protein genome-linked (vpg) an ...	2016	26830344
structural similarities and differences between two functionally distinct seca proteins, mycobacterium tuberculosis seca1 and seca2.	while seca is the atpase component of the major bacterial secretory (sec) system, mycobacteria and some gram-positive pathogens have a second paralog, seca2. in bacteria with two seca paralogs, each seca is functionally distinct, and they cannot compensate for one another. compared to seca1, seca2 exports a distinct and smaller set of substrates, some of which have roles in virulence. in the mycobacterial system, some seca2-dependent substrates lack a signal peptide, while others contain a signa ...	2016	26668263
acetylome analysis reveals the involvement of lysine acetylation in biosynthesis of antibiotics in bacillus amyloliquefaciens.	lysine acetylation is a major post-translational modification that plays an important regulatory role in almost every aspects in both eukaryotes and prokaryotes. bacillus amyloliquefaciens, a gram-positive bacterium, is very effective for the control of plant pathogens. however, very little is known about the function of lysine acetylation in this organism. here, we conducted the first lysine acetylome in b. amyloliquefaciens through a combination of highly sensitive immune-affinity purification ...	2016	26822828
a structural view of microrna-target recognition.	it is well established that the correct identification of the messenger rna targeted by a given microrna (mirna) is a difficult problem, and that available methods all suffer from low specificity. we hypothesize that the correct identification of the pairing should take into account the effect of the argonaute protein (ago), an essential catalyst of the recognition process. therefore, we developed a strategy named miren for building and scoring three-dimensional models of the ternary complex for ...	2016	26825463
systems-wide prediction of enzyme promiscuity reveals a new underground alternative route for pyridoxal 5'-phosphate production in e. coli.	recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. understanding the role of such enzymes is an important open question in biology. here we develop a genome-wide method, proper, that uses a permissive psi-blast approach to predict promiscuous activities of metabolic genes. enzyme promiscuity is typically studied experimentally using multicopy suppression, in which over-expression of a promiscuous 'replacer' gene rescues lethality caused by ina ...	2016	26821166
biological nanomotors with a revolution, linear, or rotation motion mechanism.	the ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. in 2013, a third type of biomotor, revolution without rotation (http://rnanano.osu.edu/movie.html), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded dna (dsdna) bacteriophages. this review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and en ...	2016	26819321
structural insights into the quaternary catalytic mechanism of hexameric human quinolinate phosphoribosyltransferase, a key enzyme in de novo nad biosynthesis.	quinolinate phosphoribosyltransferase (qprt) catalyses the production of nicotinic acid mononucleotide, a precursor of de novo biosynthesis of the ubiquitous coenzyme nicotinamide adenine dinucleotide. qprt is also essential for maintaining the homeostasis of quinolinic acid in the brain, a possible neurotoxin causing various neurodegenerative diseases. although qprt has been extensively analysed, the molecular basis of the reaction catalysed by human qprt remains unclear. here, we present the c ...	2016	26805589
structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition.	with bacterial resistance becoming a serious threat to global public health, antimicrobial peptides (amps) have become a promising area of focus in antibiotic research. amps are derived from a diverse range of species, from prokaryotes to humans, with a mechanism of action that often involves disruption of the bacterial cell membrane. proline-rich antimicrobial peptides (pramps) are instead actively transported inside the bacterial cell where they bind and inactivate specific targets. recently, ...	2016	26809677
multiple nucleic acid cleavage modes in divergent type iii crispr systems.	crispr-cas is an rna-guided adaptive immune system that protects bacteria and archaea from invading nucleic acids. type iii systems (cmr, csm) have been shown to cleave rna targets in vitro and some are capable of transcription-dependent dna targeting. the crenarchaeon sulfolobus solfataricus has two divergent subtypes of the type iii system (sso-iiid and a cmr7-containing variant of sso-iiib). here, we report that both the sso-iiid and sso-iiib complexes cleave cognate rna targets with a ruler ...	2016	26801642
novel base-pairing interactions at the trna wobble position crucial for accurate reading of the genetic code.	posttranscriptional modifications at the wobble position of transfer rnas play a substantial role in deciphering the degenerate genetic code on the ribosome. the number and variety of modifications suggest different mechanisms of action during messenger rna decoding, of which only a few were described so far. here, on the basis of several 70s ribosome complex x-ray structures, we demonstrate how escherichia coli trna(lys)(uuu) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)u) at ...	2016	26791911
structure of the mammalian antimicrobial peptide bac7(1-16) bound within the exit tunnel of a bacterial ribosome.	proline-rich antimicrobial peptides (pramps) produced as part of the innate immune response of animals, insects and plants represent a vast, untapped resource for the treatment of multidrug-resistant bacterial infections. pramps such as oncocin or bactenecin-7 (bac7) interact with the bacterial ribosome to inhibit translation, but their supposed specificity as inhibitors of bacterial rather than mammalian protein synthesis remains unclear, despite being key to developing drugs with low toxicity. ...	2016	26792896
centers of motion associated with ef-tu binding to the ribosome.	structural centers of motion (pivot points) in the ribosome have recently been identified by measurement of conformational changes in rrna resulting from ef-g gtp hydrolysis. this series of measurements is extended here to the ribosome's interactions with the cofactor ef-tu. four recent ef-tu bound ribosome structures were compared to unbound structures. a total of 16 pivots were identified, of which 4 are unique to the ef-tu interaction. pivots in the gtpase associated center and the sarcin-ric ...	2016	26786136
a target-protection mechanism of antibiotic resistance at atomic resolution: insights into fusb-type fusidic acid resistance.	antibiotic resistance in clinically important bacteria can be mediated by proteins that physically associate with the drug target and act to protect it from the inhibitory effects of an antibiotic. we present here the first detailed structural characterization of such a target protection mechanism mediated through a protein-protein interaction, revealing the architecture of the complex formed between the fusb fusidic acid resistance protein and the drug target (ef-g) it acts to protect. binding ...	2016	26781961
the dna polymerase iii holoenzyme contains γ and is not a trimeric polymerase.	there is widespread agreement that the clamp loader of the escherichia coli replicase has the composition dnax3δδ'χψ. two dnax proteins exist in e. coli, full length τ and a truncated γ that is created by ribosomal frameshifting. τ binds dna polymerase iii tightly; γ does not. there is a controversy as to whether or not dna polymerase iii holoenzyme (pol iii he) contains γ. a three-τ form of pol iii he would contain three pol iiis. proponents of the three-τ hypothesis have claimed that γ found i ...	2016	26786318
n(6)-methyladenosine in mrna disrupts trna selection and translation-elongation dynamics.	n(6)-methylation of adenosine (forming m(6)a) is the most abundant post-transcriptional modification within the coding region of mrna, but its role during translation remains unknown. here, we used bulk kinetic and single-molecule methods to probe the effect of m(6)a in mrna decoding. although m(6)a base-pairs with uridine during decoding, as shown by x-ray crystallographic analyses of thermus thermophilus ribosomal complexes, our measurements in an escherichia coli translation system revealed t ...	2016	26751643
two-dimensional crystallization of monomeric bovine cytochrome c oxidase with bound cytochrome c in reconstituted lipid membranes.	mitochondrial cytochrome c oxidase utilizes electrons provided by cytochrome c for the active vectorial transport of protons across the inner mitochondrial membrane through the reduction of molecular oxygen to water. direct structural evidence on the transient cytochrome c oxidase-cytochrome c complex thus far, however, remains elusive and its physiological relevant oligomeric form is unclear. here, we report on the 2d crystallization of monomeric bovine cytochrome c oxidase with tightly bound c ...	2016	26754561
the bioactive secondary metabolites from talaromyces species.	the focus of this review is placed on the chemical structures from the species of the genus talaromyces reported with reference to their biological activities. 221 secondary metabolites, including 43 alkaloids and peptides, 88 esters, 31 polyketides, 19 quinones, 15 steroid and terpenoids, and 25 other structure type compounds, have been included, and 66 references are cited.	2016	26746215
a model for genesis of transcription systems.	repeating sequences generated from rna gene fusions/ligations dominate ancient life, indicating central importance of building structural complexity in evolving biological systems. a simple and coherent story of life on earth is told from tracking repeating motifs that generate α/β proteins, 2-double-ψ-β-barrel (dpbb) type rna polymerases (rnaps), general transcription factors (gtfs), and promoters. a general rule that emerges is that biological complexity that arises through generation of repea ...	2016	26735411
redirection of the reaction specificity of a thermophilic acetolactate synthase toward acetaldehyde formation.	acetolactate synthase and pyruvate decarboxylase are thiamine pyrophosphate-dependent enzymes that convert pyruvate into acetolactate and acetaldehyde, respectively. although the former are encoded in the genomes of many thermophiles and hyperthermophiles, the latter has been found only in mesophilic organisms. in this study, the reaction specificity of acetolactate synthase from thermus thermophilus was redirected to catalyze acetaldehyde formation to develop a thermophilic pyruvate decarboxyla ...	2016	26731734
watson-crick-like pairs in ccug repeats: evidence for tautomeric shifts or protonation.	rna transcripts that include expanded ccug repeats are associated with myotonic dystrophy type 2. crystal structures of two ccug-containing oligomers show that the rna strands associate into slipped duplexes that contain noncanonical c-u pairs that have apparently undergone tautomeric transition or protonation resulting in an unusual watson-crick-like pairing. the overhanging ends of the duplexes interact forming u-u pairs, which also show tautomerism. duplexes consisting of ccug repeats are the ...	2016	26543073
complete kinetic mechanism for recycling of the bacterial ribosome.	how ef-g and rrf act together to split a post-termination ribosomal complex into its subunits has remained obscure. here, using stopped-flow experiments with rayleigh light scattering detection and quench-flow experiments with radio-detection of gtp hydrolysis, we have clarified the kinetic mechanism of ribosome recycling and obtained precise estimates of its kinetic parameters. ribosome splitting requires that ef-g binds to an already rrf-containing ribosome. ef-g binding to rrf-free ribosomes ...	2016	26527791
the nucleotide excision repair pathway protects borrelia burgdorferi from nitrosative stress in ixodes scapularis ticks.	the lyme disease spirochete borrelia burgdorferi encounters a wide range of environmental conditions as it cycles between ticks of the genus ixodes and its various mammalian hosts. reactive oxygen species (ros) and reactive nitrogen species (rns) are potent antimicrobial molecules generated during the innate immune response to infection, however, it is unclear whether ros and rns pose a significant challenge to b. burgdorferi in vivo. in this study, we screened a library of b. burgdorferi strain ...	2016	27656169
challenges with using names to link digital biodiversity information.		2016	27346955
independent evolution of six families of halogenating enzymes.	halogenated natural products are widespread in the environment, and the halogen atoms are typically vital to their bioactivities. thus far, six families of halogenating enzymes have been identified: cofactor-free haloperoxidases (hpo), vanadium-dependent haloperoxidases (v-hpo), heme iron-dependent haloperoxidases (hi-hpo), non-heme iron-dependent halogenases (ni-hg), flavin-dependent halogenases (f-hg), and s-adenosyl-l-methionine (sam)-dependent halogenases (s-hg). however, these halogenating ...	2016	27153321
bacterial gcn5-related n-acetyltransferases: from resistance to regulation.	the gcn5-related n-acetyltransferases family (gnat) is an important family of proteins that includes more than 100000 members among eukaryotes and prokaryotes. acetylation appears as a major regulatory post-translational modification and is as widespread as phosphorylation. n-acetyltransferases transfer an acetyl group from acetyl-coa to a large array of substrates, from small molecules such as aminoglycoside antibiotics to macromolecules. acetylation of proteins can occur at two different posit ...	2016	26818562
neisseria meningitidis translation elongation factor p and its active-site arginine residue are essential for cell viability.	translation elongation factor p (ef-p), a ubiquitous protein over the entire range of bacterial species, rescues ribosomal stalling at consecutive prolines in proteins. in escherichia coli and salmonella enterica, the post-translational β-lysyl modification of lys34 of ef-p is important for the ef-p activity. the β-lysyl ef-p modification pathway is conserved among only 26-28% of bacteria. recently, it was found that the shewanella oneidensis and pseudomonas aeruginosa ef-p proteins, containing ...	2016	26840407
dcia is an ancestral replicative helicase operator essential for bacterial replication initiation.	delivery of the replicative helicase onto dna is an essential step in the initiation of replication. in bacteria, dnac (in escherichia coli) and dnai (in bacillus subtilis) are representative of the two known mechanisms that assist the replicative helicase at this stage. here, we establish that these two strategies cannot be regarded as prototypical of the bacterial domain since dnac and dnai (dna[ci]) are present in only a few bacterial phyla. we show that dna[ci] was domesticated at least seve ...	2016	27830752
driving apart and segregating genomes in archaea.	genome segregation is a fundamental biological process in organisms from all domains of life. how this stage of the cell cycle unfolds in eukarya has been clearly defined and considerable progress has been made to unravel chromosome partition in bacteria. the picture is still elusive in archaea. the lineages of this domain exhibit different cell-cycle lifestyles and wide-ranging chromosome copy numbers, fluctuating from 1 up to 55. this plurality of patterns suggests that a variety of mechanisms ...	2016	27450111
mglc, a paralog of myxococcus xanthus gtpase-activating protein mglb, plays a divergent role in motility regulation.	in order to optimize interactions with their environment and one another, bacteria regulate their motility. in the case of the rod-shaped cells of myxococcus xanthus, regulated motility is essential for social behaviors. m. xanthus moves over surfaces using type iv pilus-dependent motility and gliding motility. these two motility systems are coordinated by a protein module that controls cell polarity and consists of three polarly localized proteins, the small g protein mgla, the cognate mgla gtp ...	2016	26574508