Abstract:
BACKGROUND:S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-producing strain (E3) obtained by random mutagenesis and screening from the wild-type strain NRRL23338, and examined time-series expression profiles of both E3 and NRRL23338. Based on the genomic data and transcriptpmic data of these two strains, we carried out comparative analysis of high-producing strain and wild-type strain at both the genomic level and the transcriptomic level. RESULTS:We observed a large number of genetic variants including 60 insertions, 46 deletions and 584 single nucleotide variations (SNV) in E3 in comparison with NRRL23338, and the analysis of time series transcriptomic data indicated that the genes involved in erythromycin biosynthesis and feeder pathways were significantly up-regulated during the 60 hours time-course. According to our data, BldD, a previously identified ery cluster regulator, did not show any positive correlations with the expression of ery cluster, suggesting the existence of alternative regulation mechanisms of erythromycin synthesis in S. erythraea. Several potential regulators were then proposed by integration analysis of genomic and transcriptomic data. CONCLUSION:This is a demonstration of the functional comparative genomics between an industrial S. erythraea strain and the wild-type strain. These findings help to understand the global regulation mechanisms of erythromycin biosynthesis in S. erythraea, providing useful clues for genetic and metabolic engineering in the future.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Li YY,Chang X,Yu WB,Li H,Ye ZQ,Yu H,Liu BH,Zhang Y,Zhang SL,Ye BC,Li YXdoi
10.1186/1471-2164-14-523subject
Has Abstractpub_date
2013-07-31 00:00:00pages
523issn
1471-2164pii
1471-2164-14-523journal_volume
14pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Carrot (Daucus carota) is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction of foreign genes, especially for oral delivery of vaccines and other therapeutic proteins. Until recently efforts to express recombi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-222
更新日期:2006-08-31 00:00:00
abstract:BACKGROUND:Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have ana...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-123
更新日期:2005-09-14 00:00:00
abstract:BACKGROUND:Elucidating the candidate genes and key metabolites responsible for pulp and peel coloration is essential for breeding pitaya fruit with new and improved appeal and high nutritional value. Here, we used transcriptome (RNA-Seq) and metabolome analysis (UPLC-MS/MS) to identify structural and regulatory genes a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07133-5
更新日期:2020-10-22 00:00:00
abstract::Following the publication of the original article [1], the authors reported an error in Fig. 2 of the PDF version of their article. ...
journal_title:BMC genomics
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12864-019-6419-1
更新日期:2019-12-31 00:00:00
abstract:BACKGROUND:We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments. RESULTS:By using simulated and real datasets we showed that our tool, based on read count approac...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4137-0
更新日期:2017-09-21 00:00:00
abstract:BACKGROUND:The MYB superfamily is one of the most abundant transcription factor (TF) families in plants. MYB proteins include highly conserved N-terminal MYB repeats (1R, R2R3, 3R, and atypical) and various C-terminal sequences that confer extensive functions. However, the functions of most MYB genes are unknown, and h...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1216-y
更新日期:2015-01-23 00:00:00
abstract:BACKGROUND:Retrogenes are processed copies of other genes. This duplication mechanism produces a copy of the parental gene that should not contain introns, and usually does not contain cis-regulatory regions. Here, we computationally address the evolutionary origin of promoter and other cis-regulatory regions in retrog...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-241
更新日期:2008-05-22 00:00:00
abstract:BACKGROUND:Aeromonas salmonicida subsp. salmonicida is a ubiquitous psychrophilic waterborne bacterium and a fish pathogen. The numerous mobile elements, especially insertion sequences (IS), in its genome promote rearrangements that impact its phenotype. One of the main virulence factors of this bacterium, its type thr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3921-1
更新日期:2017-07-12 00:00:00
abstract:BACKGROUND:In contrast to unidirectional promoters wherein antisense transcription results in short transcripts which are rapidly degraded, bidirectional promoters produce mature transcripts in both sense and antisense orientation. To understand the molecular mechanism of how productive bidirectional transcription is r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4697-7
更新日期:2018-05-02 00:00:00
abstract:BACKGROUND:In mammalian cells changes in intracellular pH (pHi), which are predominantly controlled by activity of plasma membrane ion exchangers, regulate a diverse range of normal and pathological cellular processes. How changes in pHi affect distinct cellular processes has primarily been determined by evaluating pro...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-5-46
更新日期:2004-07-16 00:00:00
abstract:BACKGROUND:Existing functional description of genes are categorical, discrete, and mostly through manual process. In this work, we explore the idea of gene embedding, distributed representation of genes, in the spirit of word embedding. RESULTS:From a pure data-driven fashion, we trained a 200-dimension vector represe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5370-x
更新日期:2019-02-04 00:00:00
abstract:BACKGROUND:Mycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic analyses, repetitive sequences are associated with transposable elements (TEs). TEs are dispersed ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-720
更新日期:2012-12-22 00:00:00
abstract:BACKGROUND:The Bacillus cereus sensu lato group currently includes seven species (B. cereus, B. anthracis, B. mycoides, B. pseudomycoides, B. thuringiensis, B. weihenstephanensis and B. cytotoxicus) that recent phylogenetic and phylogenomic analyses suggest are likely a single species, despite their varied phenotypes. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-564
更新日期:2012-10-22 00:00:00
abstract:BACKGROUND:Theileria parva is an intracellular parasite that causes a lymphoproliferative disease in cattle. It does so by inducing cancer-like phenotypes in the host cells it infects, although the molecular and regulatory mechanisms involved remain poorly understood. RNAseq data, and the resulting updated genome annot...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2444-5
更新日期:2016-02-20 00:00:00
abstract:BACKGROUND:High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in that gene's probe set will provide a consistent message signifying the gene's p...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-613
更新日期:2008-12-18 00:00:00
abstract:BACKGROUND:Spinal cord injury leads to neurological dysfunctions affecting the motor, sensory as well as the autonomic systems. Increased excitability of motor neurons has been implicated in injury-induced spasticity, where the reappearance of self-sustained plateau potentials in the absence of modulatory inputs from t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-365
更新日期:2010-06-09 00:00:00
abstract:BACKGROUND:As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the hospital-associated isolates and ignored isolates originated from the natural environments. RESULTS:In this study, comparative genomic analysis ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5975-8
更新日期:2019-07-22 00:00:00
abstract:BACKGROUND:Restriction-modification (R-M) systems protect bacteria and archaea from attacks by bacteriophages and archaeal viruses. An R-M system specifically recognizes short sites in foreign DNA and cleaves it, while such sites in the host DNA are protected by methylation. Prokaryotic viruses have developed a number ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5324-3
更新日期:2018-12-07 00:00:00
abstract::ᅟ: Upon publication of the original article [1], the authors had flagged that there was an error in Fig. 1c, as the key in this figure was displaying incorrectly. The colours had not displayed in the key in the final published article, and instead appear as plain white. ...
journal_title:BMC genomics
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12864-018-4614-0
更新日期:2018-04-11 00:00:00
abstract::An amendment to this paper has been published and can be accessed via the original article. ...
journal_title:BMC genomics
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12864-020-6754-2
更新日期:2020-06-03 00:00:00
abstract:BACKGROUND:Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopoly...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4544-x
更新日期:2018-02-21 00:00:00
abstract:BACKGROUND:Genome-scale functional genomic screens across large cell line panels provide a rich resource for discovering tumor vulnerabilities that can lead to the next generation of targeted therapies. Their data analysis typically has focused on identifying genes whose knockdown enhances response in various pre-defin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2807-y
更新日期:2016-06-13 00:00:00
abstract:BACKGROUND:Alternative polyadenylation (APA) has emerged as a pervasive mechanism that contributes to the transcriptome complexity and dynamics of gene regulation. The current tsunami of whole genome poly(A) site data from various conditions generated by 3' end sequencing provides a valuable data source for the study o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5433-7
更新日期:2019-01-22 00:00:00
abstract:BACKGROUND:Fusarium verticillioides causes ear rot in maize (Zea mays L.) and accumulation of mycotoxins, that affect human and animal health. Currently, chemical and agronomic measures to control Fusarium ear rot are not very effective and selection of more resistant genotypes is a desirable strategy to reduce contami...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-710
更新日期:2014-08-25 00:00:00
abstract:BACKGROUND:Mitochondria are organelles that fulfill a fundamental role in cell bioenergetics, as well as in other processes like cell signaling and death. Small non-coding RNAs (sncRNA) are now being considered as pivotal post-transcriptional regulators, widening the landscape of their diversity and functions. In mamma...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5020-3
更新日期:2018-08-28 00:00:00
abstract:BACKGROUND:Heat shock proteins (Hsps) are molecular chaperones that are involved in many normal cellular processes and stress responses, and heat shock factors (Hsfs) are the transcriptional activators of Hsps. Hsfs and Hsps are widely coordinated in various biological processes. Although the roles of Hsfs and Hsps in ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1398-3
更新日期:2015-03-14 00:00:00
abstract:BACKGROUND:Epidermal Growth Factor (EGF) is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-326
更新日期:2011-06-23 00:00:00
abstract:BACKGROUND:Acinetobacter baumannii is a major health problem. The most common infection caused by A. baumannii is hospital acquired pneumonia, and the associated mortality rate is approximately 50%. Neither in vivo nor ex vivo expression profiling has been performed at the proteomic or transcriptomic level for pneumoni...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1608-z
更新日期:2015-05-30 00:00:00
abstract:BACKGROUND:Color polymorphism in the nacre of pteriomorphian bivalves is of great interest for the pearl culture industry. The nacreous layer of the Polynesian black-lipped pearl oyster Pinctada margaritifera exhibits a large array of color variation among individuals including reflections of blue, green, yellow and pi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1776-x
更新日期:2015-08-01 00:00:00
abstract:BACKGROUND:The pituitary is a critical neuroendocrine gland that is comprised of five hormone-secreting cell types, which develops in tandem during the embryonic stage. Some essential genes have been identified in the early stage of adenohypophysial development, such as PITX1, FGF8, BMP4 and SF-1. However, it is likely...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-109
更新日期:2009-03-15 00:00:00