Abstract：
:High-throughput identification of proteins and their accurate partial sequencing by shotgun nanoLC-MS/MS are now feasible for any cellular model at a full genomic scale. Proteogenomics is the integration of these data with the genome. Mining microbial proteomes allows validation of predicted orphan genes and correction of genome annotation errors such as discovery of unannotated genes, reversal of reading frames and identification of translational start sites, stop codon read-throughs or programmed frameshifts. Recent advances have been achieved in database searches, N-terminal oriented proteomics and homology-driven proteogenomics. From now on, proteogenomics on newly sequenced model genomes can be carried out at the earliest stage of the genome project as already exemplified by Mycoplasma mobile and Deinococcus deserti genomes. The proteomics and genomics alliance produces almost complete and accurate gene catalogues for small microbial genomes, a comprehensiveness which is essential for efficient systems biology.
journal_name
Curr Opin Microbioljournal_title
Current opinion in microbiologyauthors
Armengaud Jdoi
10.1016/j.mib.2009.03.005subject
Has Abstractpub_date
2009-06-01 00:00:00pages
292-300issue
3eissn
1369-5274issn
1879-0364pii
S1369-5274(09)00040-Xjournal_volume
12pub_type
杂志文章,评审abstract：:Analyses of the complex regulatory networks leading to T cell survival, death, and immune deficiency have been aided in the past year by the dramatic development of new technologies to identify T cells and assess T cell function. These new techniques have shown that functional inactivation and apoptotic elimination of...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(99)80067-8
更新日期：1999-08-01 00:00:00
abstract：:We postulate that phenotypic resistance to antibiotics, persistence, is not an evolved (selected-for) character but rather like mutation, an inadvertent product of different kinds of errors and glitches. The rate of generation of these errors is augmented by exposure to these drugs. The genes that have been identified...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2014.06.016
更新日期：2014-10-01 00:00:00
abstract：:The skin is our first line of defense, protecting us from invasion and evaporation. Its variable structure, changing geography, and complex immune repertoire provide a vast interface for our cutaneous microbial community. Skin is inhabited by many thousands of microbes, but this review focuses on the dominant eukaryot...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2017.10.024
更新日期：2017-12-01 00:00:00
abstract：:Biochemical, serological and microbiological methods have been used to dissect pathogens and identify the components useful for vaccine development. Although successful in many cases, this approach is time-consuming and fails when the pathogens cannot be cultivated in vitro, or when the most abundant antigens are vari...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(00)00119-3
更新日期：2000-10-01 00:00:00
abstract：:Kinetoplastid parasites adapt to different environments with wide-reaching control of gene expression, but transcription of nuclear protein-coding genes is polycistronic: there is no individual control of transcription initiation. Mature mRNAs are made by co-transcriptional trans splicing and polyadenylation, and comp...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2016.04.018
更新日期：2016-08-01 00:00:00
abstract：:In part, members of the genus Streptomyces have been studied because they produce many important secondary metabolites with antibiotic activity and for the interest in their relatively elaborate life cycle. These sporulating filamentous bacteria are remarkably synchronous for division and genome segregation in special...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2009.10.004
更新日期：2009-12-01 00:00:00
abstract：:Candida albicans is a regular member of the intestinal microbiota in the majority of the human population. This underscores C. albicans' adaptation to life in the intestine without inducing competitive interactions with other microbes, or immune responses detrimental to its survival. However, specific conditions such ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2020.05.006
更新日期：2020-08-01 00:00:00
abstract：:Streptococcus agalactiae (group B Streptococcus, GBS), a normal constituent of the intestinal microbiota is the major cause of human neonatal infections and a worldwide spread 'hypervirulent' clone, GBS ST-17, is strongly associated with neonatal meningitis. Adhesion to epithelial and endothelial cells constitutes a k...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2011.12.002
更新日期：2012-02-01 00:00:00
abstract：:Quorum sensing is an important mechanism for the regulation of genes in many Gram-negative and Gram-positive bacteria. In the opportunistic pathogen Pseudomonas aeruginosa, the absence of one or more components of the quorum-sensing system results in a significant reduction in virulence. Recent advances in the past ye...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(03)00008-0
更新日期：2003-02-01 00:00:00
abstract：:Gene clusters contributing to processes such as cell growth and pathogenicity are often controlled by two-component signal transduction systems (TCSs). Specific inhibitors against TCS systems work differently from conventional antibiotics, and developing them into new drugs that are effective against various drug-resi...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2010.01.008
更新日期：2010-04-01 00:00:00
abstract：:Recent work has shown that Immunoglobulin-like (Ig-like) domains occur frequently on the surface of tailed dsDNA bacteriophages. Several of these Ig-like domains are added to bacteriophage structural proteins via programmed ribosomal frameshifts, and their evolutionary patterns suggest that they can be exchanged by ho...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2007.05.018
更新日期：2007-08-01 00:00:00
abstract：:There is accumulating evidence that motile bacteria are chemotactically attracted to environmental pollutants that they can degrade. Chemotaxis, the ability of motile bacteria to detect and respond to specific chemicals in the environment, can increase an organism's chances of locating useful sources of carbon, nitrog...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(02)00320-x
更新日期：2002-06-01 00:00:00
abstract：:Biofilm development and quorum sensing (QS) are closely interconnected processes. Biofilm formation is a cooperative group behaviour that involves bacterial populations living embedded in a self-produced extracellular matrix. QS is a cell-cell communication mechanism that synchronizes gene expression in response to po...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2014.02.008
更新日期：2014-04-01 00:00:00
abstract：:In Gram-negative bacteria such as Escherichia coli the peptidoglycan sacculus resides in the periplasm, a compartment that experiences changes in pH value, osmolality, ion strength and other parameters depending on the cell's environment. Hence, the cell needs robust peptidoglycan growth mechanisms to grow and divide ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2017.01.006
更新日期：2017-04-01 00:00:00
abstract：:Toxin-antitoxin (TA) systems are small genetic modules that are abundant in bacterial genomes. Three types have been described so far, depending on the nature and mode of action of the antitoxin component. While type II systems are surprisingly highly represented because of their capacity to move by horizontal gene tr...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2010.10.006
更新日期：2010-12-01 00:00:00
abstract：:The détente between pathogen and host has been of keen interest to researchers in spite of being exceedingly difficult to probe. Recently, new RNA interference (RNAi) technologies, in particular in Drosophila tissue culture cells, have made it possible to interrogate the genetics of host organisms rapidly, with nearly...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2008.05.007
更新日期：2008-06-01 00:00:00
abstract：:Organisms do not exist isolated from each other, but constantly interact. Cells can sense the presence of interaction partners by a range of receptors and, via complex regulatory networks, specifically react by changing the expression of many of their genes. Technological advances in next-generation sequencing over th...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2017.09.001
更新日期：2018-04-01 00:00:00
abstract：:The genomic revolution is fully upon us in 2006 and the pace of discovery is set to accelerate with the emergence of ultra-high-throughput sequencing technologies. Our complete genome collection of bacteria and archaea continues to grow in number and diversity, as genome sequencing is applied to an array of new proble...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2006.08.008
更新日期：2006-10-01 00:00:00
abstract：:Atomic force microscopy imaging and force spectroscopy have recently opened a range of novel applications in microbiology. During the past two years, rapid advances have been made using atomic force microscopy to visualize the surface structure of two-dimensional bacterial protein crystals, biofilms and individual cel...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(03)00058-4
更新日期：2003-06-01 00:00:00
abstract：:The enzymological and genetic aspects of microbial metabolism of hydrocarbons have been extensively revealed. Such molecular information is useful for understanding the bioremediation of oil spill environments and production of hydrocarbon-specific fine chemicals. ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(03)00053-5
更新日期：2003-06-01 00:00:00
abstract：:Gram-positive pathogens are a major cause of community-acquired and hospital-acquired infections, and exhibit a remarkable ability to develop antibiotic resistance. Methicillin-resistant Staphylococcus aureus (MRSA), glycopeptide-resistant enterococci (GRE) and multidrug-resistant pneumococci are currently the major r...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2010.08.006
更新日期：2010-10-01 00:00:00
abstract：:Research into the mechanisms regulating bacterial cell size has its origins in a single paper published over 50 years ago. In it Schaechter and colleagues made the observation that the chemical composition and size of a bacterial cell is a function of growth rate, independent of the medium used to achieve that growth ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2015.01.011
更新日期：2015-04-01 00:00:00
abstract：:The quest for the discovery of novel natural products has entered a new chapter with the enormous wealth of genetic data that is now available. This information has been exploited by using whole-genome sequence mining to uncover cryptic pathways, or biosynthetic pathways for previously undetected metabolites. Alternat...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2006.04.002
更新日期：2006-06-01 00:00:00
abstract：:Elimination of non-functional or unwanted proteins is critical for cell growth and regulation. In bacteria, ATP-dependent proteases target cytoplasmic proteins for degradation, contributing to both protein quality control and regulation of specific proteins, thus playing roles parallel to that of the proteasome in euk...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2013.01.002
更新日期：2013-04-01 00:00:00
abstract：:Eukaryotes host numerous intracellular and associated microbes in their microbiota. Fungi, the so-called Mycobiota, are important members of both human and plant microbiota. Moreover, members of the plant mycobiota host their own microbiota on their surfaces and inside their hyphae. The microbiota of the mycobiota inc...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2019.08.004
更新日期：2019-06-01 00:00:00
abstract：:Septins are cytoskeletal elements that contain a highly conserved canonical G domain flanked by more divergent N- and C-termini. Septin monomers form heteropolymers that in turn associate into a variety of higher-order structures. SUMOylation, acetylation and phosphorylation of septins have all been reported; however,...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2012.09.007
更新日期：2012-12-01 00:00:00
abstract：:Environmental pathogenic fungi present a paradox in that they are virulent in animals without requiring animal hosts for replication or survival, a phenomenon we call 'ready-made' virulence. In the human pathogenic fungus Cryptococcus neoformans, the capacity for virulence in animals may originate from environmental s...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(03)00082-1
更新日期：2003-08-01 00:00:00
abstract：:Pseudogenes are defined as fragments of once-functional genes that have been silenced by one or more nonsense, frameshift or missense mutations. Despite continuing increases in the speed of sequencing and annotating bacterial genomes, the identification and categorisation of pseudogenes remains problematic. Even when ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2014.11.012
更新日期：2015-02-01 00:00:00
abstract：:Integrative and conjugative elements (ICEs) are nearly ubiquitous in microbial genomes and influence their evolution by providing adaptive functions to their host and by enhancing genome plasticity and diversification. For a long-time, it has been assumed that by integrating into the chromosome of their host, these se...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2017.03.014
更新日期：2017-08-01 00:00:00
abstract：:Cyanobacteria possess the simplest known circadian clock, which presents a unique opportunity to study how rhythms are generated and how input signals from the environment reset the clock time. The kaiABC locus forms the core of the oscillator, and the remarkable ability to reconstitute oscillations using purified Kai...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2014.02.010
更新日期：2014-04-01 00:00:00
