A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production.


BACKGROUND:Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi-billion dollar petrochemical market into one based on renewable resources. Actinobacillus succinogenes naturally converts sugars and CO2 into high concentrations of succinic acid as part of a mixed-acid fermentation. Efforts are ongoing to maximize carbon flux to succinate to achieve an industrial process. RESULTS:Described here is the 2.3 Mb A. succinogenes genome sequence with emphasis on A. succinogenes's potential for genetic engineering, its metabolic attributes and capabilities, and its lack of pathogenicity. The genome sequence contains 1,690 DNA uptake signal sequence repeats and a nearly complete set of natural competence proteins, suggesting that A. succinogenes is capable of natural transformation. A. succinogenes lacks a complete tricarboxylic acid cycle as well as a glyoxylate pathway, and it appears to be able to transport and degrade about twenty different carbohydrates. The genomes of A. succinogenes and its closest known relative, Mannheimia succiniciproducens, were compared for the presence of known Pasteurellaceae virulence factors. Both species appear to lack the virulence traits of toxin production, sialic acid and choline incorporation into lipopolysaccharide, and utilization of hemoglobin and transferrin as iron sources. Perspectives are also given on the conservation of A. succinogenes genomic features in other sequenced Pasteurellaceae. CONCLUSIONS:Both A. succinogenes and M. succiniciproducens genome sequences lack many of the virulence genes used by their pathogenic Pasteurellaceae relatives. The lack of pathogenicity of these two succinogens is an exciting prospect, because comparisons with pathogenic Pasteurellaceae could lead to a better understanding of Pasteurellaceae virulence. The fact that the A. succinogenes genome encodes uptake and degradation pathways for a variety of carbohydrates reflects the variety of carbohydrate substrates available in the rumen, A. succinogenes's natural habitat. It also suggests that many different carbon sources can be used as feedstock for succinate production by A. succinogenes.


BMC Genomics


BMC genomics


McKinlay JB,Laivenieks M,Schindler BD,McKinlay AA,Siddaramappa S,Challacombe JF,Lowry SR,Clum A,Lapidus AL,Burkhart KB,Harkins V,Vieille C




Has Abstract


2010-11-30 00:00:00










  • Genome-wide analysis of purple acid phosphatase structure and expression in ten vegetable species.

    abstract:BACKGROUND:Acquisition of external phosphorus (P) and optimisation of internal P are essential for plant growth and development, and insufficient availability of P in soils is a major challenge in agriculture. Members of the purple acid phosphatase (PAP) family of enzymes are candidates for increasing P use efficiency....

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Xie L,Shang Q

    更新日期:2018-08-31 00:00:00

  • Genomic characterization of ribitol teichoic acid synthesis in Staphylococcus aureus: genes, genomic organization and gene duplication.

    abstract:BACKGROUND:Staphylococcus aureus or MRSA (Methicillin Resistant S. aureus), is an acquired pathogen and the primary cause of nosocomial infections worldwide. In S. aureus, teichoic acid is an essential component of the cell wall, and its biosynthesis is not yet well characterized. Studies in Bacillus subtilis have disc...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Qian Z,Yin Y,Zhang Y,Lu L,Li Y,Jiang Y

    更新日期:2006-04-05 00:00:00

  • Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

    abstract:BACKGROUND:Genetic influences underpinning complex traits are thought to involve multiple quantitative trait loci (QTLs) of small effect size. Detection of such QTL associations requires systematic screening of large numbers of DNA markers within large sample populations. Using pooled DNA on SNP microarrays to screen f...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Docherty SJ,Butcher LM,Schalkwyk LC,Plomin R

    更新日期:2007-07-04 00:00:00

  • RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean.

    abstract:BACKGROUND:Oxidative stress caused by ground level ozone is a contributor to yield loss in a number of important crop plants. Soybean (Glycine max) is considered to be ozone sensitive, and current research into its response to oxidative stress is limited. To better understand the genetic response in soybean to oxidativ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Whaley A,Sheridan J,Safari S,Burton A,Burkey K,Schlueter J

    更新日期:2015-06-04 00:00:00

  • Concurrent host-pathogen gene expression in the lungs of pigs challenged with Actinobacillus pleuropneumoniae.

    abstract:BACKGROUND:Actinobacillus pleuropneumoniae causes pleuropneumonia in pigs, a disease which is associated with high morbidity and mortality, as well as impaired animal welfare. To obtain in-depth understanding of this infection, the interplay between virulence factors of the pathogen and defense mechanisms of the porcin...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Brogaard L,Klitgaard K,Heegaard PM,Hansen MS,Jensen TK,Skovgaard K

    更新日期:2015-05-28 00:00:00

  • Genomic characterization of JG068, a novel virulent podovirus active against Burkholderia cenocepacia.

    abstract:BACKGROUND:As is true for many other antibiotic-resistant Gram-negative pathogens, members of the Burkholderia cepacia complex (BCC) are currently being assessed for their susceptibility to phage therapy as an antimicrobial treatment. The objective of this study was to perform genomic and limited functional characteriz...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lynch KH,Abdu AH,Schobert M,Dennis JJ

    更新日期:2013-08-27 00:00:00

  • Transcriptomic analysis of differentially expressed genes in the Ras1(CA)-overexpressed and wildtype posterior silk glands.

    abstract:BACKGROUND:Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1(CA) oncogene specifically in the posterior silk gland (PSG) improved cell growth, fibroin synthesis, and thus silk yield. However, the detailed molecula...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ma L,Ma Q,Li X,Cheng L,Li K,Li S

    更新日期:2014-03-09 00:00:00

  • MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori.

    abstract:BACKGROUND:The growth and development of the posterior silk gland and the biosynthesis of the silk core protein at the fifth larval instar stage of Bombyx mori are of paramount importance for silk production. RESULTS:Here, aided by next-generation sequencing and microarry assay, we profile 1,229 microRNAs (miRNAs), in...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li J,Cai Y,Ye L,Wang S,Che J,You Z,Yu J,Zhong B

    更新日期:2014-05-29 00:00:00

  • Correction to: De novo profiling of RNA viruses in Anopheles malaria vector mosquitoes from forest ecological zones in Senegal and Cambodia.

    abstract::Following the publication of this article [1], the authors reported that the original shading in columns 3 and 4 of Table 3, which indicated the presence or absence of viruses in each library, had been removed during typesetting. ...

    journal_title:BMC genomics

    pub_type: 杂志文章,已发布勘误


    authors: Belda E,Nanfack-Minkeu F,Eiglmeier K,Carissimo G,Holm I,Diallo M,Diallo D,Vantaux A,Kim S,Sharakhov IV,Vernick KD

    更新日期:2019-09-05 00:00:00

  • Comparative proteomics reveals that central metabolism changes are associated with resistance against Sporisorium scitamineum in sugarcane.

    abstract:BACKGROUND:Sugarcane smut, which is caused by Sporisorium scitamineum, has been threatening global sugarcane production. Breeding smut resistant sugarcane varieties has been proven to be the most effective method of controlling this particular disease. However, a lack of genome information of sugarcane has hindered the...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Su Y,Xu L,Wang Z,Peng Q,Yang Y,Chen Y,Que Y

    更新日期:2016-10-12 00:00:00

  • Arsenic-induced changes in the gene expression of lung epithelial L2 cells: implications in carcinogenesis.

    abstract:BACKGROUND:Arsenic is a carcinogen that is known to induce cell transformation and tumor formation. Although studies have been performed to examine the modulation of signaling molecules caused by arsenic exposure, the molecular mechanisms by which arsenic causes cancer are still unclear. We hypothesized that arsenic al...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Posey T,Weng T,Chen Z,Chintagari NR,Wang P,Jin N,Stricker H,Liu L

    更新日期:2008-03-03 00:00:00

  • Database of exact tandem repeats in the Zebrafish genome.

    abstract:BACKGROUND:Sequencing of the approximately 1.7 billion bases of the zebrafish genome is currently underway. To date, few high resolution genetic maps exist for the zebrafish genome, based mainly on single nucleotide polymorphisms (SNPs) and short microsatellite repeats. The desire to construct a higher resolution genet...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Rouchka EC

    更新日期:2010-06-01 00:00:00

  • Zooplankton diversity analysis through single-gene sequencing of a community sample.

    abstract:BACKGROUND:Oceans cover more than 70% of the earth's surface and are critical for the homeostasis of the environment. Among the components of the ocean ecosystem, zooplankton play vital roles in energy and matter transfer through the system. Despite their importance, understanding of zooplankton biodiversity is limited...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Machida RJ,Hashiguchi Y,Nishida M,Nishida S

    更新日期:2009-09-17 00:00:00

  • Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon.

    abstract:BACKGROUND:A key developmental transformation in the life of all vertebrates is the transition to sexual maturity, whereby individuals are capable of reproducing for the first time. In the farming of Atlantic salmon, early maturation prior to harvest size has serious negative production impacts. RESULTS:We report geno...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Mohamed AR,Verbyla KL,Al-Mamun HA,McWilliam S,Evans B,King H,Kube P,Kijas JW

    更新日期:2019-02-15 00:00:00

  • A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-Seq data.

    abstract:BACKGROUND:The recent advance of high-throughput sequencing makes it feasible to study entire transcriptomes through the application of de novo sequence assembly algorithms. While a popular strategy is to first construct an intermediate de Bruijn graph structure to represent the transcriptome, an additional step is nee...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sze SH,Tarone AM

    更新日期:2014-01-01 00:00:00

  • Expression of immune-response genes in lepidopteran host is suppressed by venom from an endoparasitoid, Pteromalus puparum.

    abstract:BACKGROUND:The relationships between parasitoids and their insect hosts have attracted attention at two levels. First, the basic biology of host-parasitoid interactions is of fundamental interest. Second, parasitoids are widely used as biological control agents in sustainable agricultural programs. Females of the grega...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Fang Q,Wang L,Zhu J,Li Y,Song Q,Stanley DW,Akhtar ZR,Ye G

    更新日期:2010-09-02 00:00:00

  • Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms.

    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


    authors: Ruhlman T,Lee SB,Jansen RK,Hostetler JB,Tallon LJ,Town CD,Daniell H

    更新日期:2006-08-31 00:00:00

  • ICPD-a new peak detection algorithm for LC/MS.

    abstract:BACKGROUND:The identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. Increasing evidence has shown that biomarkers are often low abundance proteins. However, LC/MS systems are subject to considerable noise...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhang J,Haskins W

    更新日期:2010-12-01 00:00:00

  • SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines.

    abstract:BACKGROUND:Many tools exist to predict structural variants (SVs), utilizing a variety of algorithms. However, they have largely been developed and tested on human germline or somatic (e.g. cancer) variation. It seems appropriate to exploit this wealth of technology available for humans also for other species. Objective...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Leung WY,Marschall T,Paudel Y,Falquet L,Mei H,Schönhuth A,Maoz Moss TY

    更新日期:2015-03-25 00:00:00

  • Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana.

    abstract:BACKGROUND:Modifications of RNA bases have been found in some mRNAs and non-coding RNAs including rRNAs, tRNAs, and snRNAs, where modified bases are important for RNA function. Little is known about RNA base modifications in Arabidopsis thaliana. RESULTS:In the current work, we carried out a bioinformatics analysis of...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Iida K,Jin H,Zhu JK

    更新日期:2009-04-09 00:00:00

  • Chips and tags suggest plant-environment interactions differ for two alpine Pachycladon species.

    abstract:BACKGROUND:Expression profiling has been proposed as a means for screening non-model organisms in their natural environments to identify genes potentially important in adaptive diversification. Tag profiling using high throughput sequencing is a relatively low cost means of expression profiling with deep coverage. Howe...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Voelckel C,Gruenheit N,Biggs P,Deusch O,Lockhart P

    更新日期:2012-07-19 00:00:00

  • Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems.

    abstract:BACKGROUND:Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents explora...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: O'Callaghan A,Bottacini F,O'Connell Motherway M,van Sinderen D

    更新日期:2015-10-21 00:00:00

  • Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring.

    abstract:BACKGROUND:Chloroplasts have their own genomes, independent from nuclear genomes, that play vital roles in growth, which is a major targeted trait for genetic improvement in Populus. Angiosperm chloroplast genomes are maternally inherited, but the chloroplast' variation pattern of poplar at the single-base level during...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhu S,Xu M,Wang H,Pan H,Wang G,Huang M

    更新日期:2018-05-29 00:00:00

  • Complex sense-antisense architecture of TNFAIP1/POLDIP2 on 17q11.2 represents a novel transcriptional structural-functional gene module involved in breast cancer progression.

    abstract:BACKGROUND:A sense-antisense gene pair (SAGP) is a gene pair where two oppositely transcribed genes share a common nucleotide sequence region. In eukaryotic genomes, SAGPs can be organized in complex sense-antisense architectures (CSAGAs) in which at least one sense gene shares loci with two or more antisense partners....

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Grinchuk OV,Motakis E,Kuznetsov VA

    更新日期:2010-02-10 00:00:00

  • Divergence in function and expression of the NOD26-like intrinsic proteins in plants.

    abstract:BACKGROUND:NOD26-like intrinsic proteins (NIPs) that belong to the aquaporin superfamily are plant-specific and exhibit a similar three-dimensional structure. Experimental evidences however revealed that functional divergence should have extensively occurred among NIP genes. It is therefore intriguing to further invest...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Liu Q,Wang H,Zhang Z,Wu J,Feng Y,Zhu Z

    更新日期:2009-07-15 00:00:00

  • Avoidance of recognition sites of restriction-modification systems is a widespread but not universal anti-restriction strategy of prokaryotic viruses.

    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


    authors: Rusinov IS,Ershova AS,Karyagina AS,Spirin SA,Alexeevski AV

    更新日期:2018-12-07 00:00:00

  • Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages.

    abstract:BACKGROUND:Shiga toxin producing Escherichia coli O157 can cause severe bloody diarrhea and haemolytic uraemic syndrome. Phage typing of E. coli O157 facilitates public health surveillance and outbreak investigations, certain phage types are more likely to occupy specific niches and are associated with specific age gro...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cowley LA,Beckett SJ,Chase-Topping M,Perry N,Dallman TJ,Gally DL,Jenkins C

    更新日期:2015-04-08 00:00:00

  • A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data.

    abstract:BACKGROUND:Affymetrix GeneChip typically contains multiple probe sets per gene, defined as sibling probe sets in this study. These probe sets may or may not behave similar across treatments. The most appropriate way of consolidating sibling probe sets suitable for analysis is an open problem. We propose the Analysis of...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li H,Zhu D,Cook M

    更新日期:2008-04-24 00:00:00

  • Genome-wide genetic aberrations of thymoma using cDNA microarray based comparative genomic hybridization.

    abstract:BACKGROUND:Thymoma is a heterogeneous group of tumors in biology and clinical behavior. Even though thymoma is divided into five subgroups following the World Health Organization classification, the nature of the disease is mixed within the subgroups. RESULTS:We investigated the molecular characteristics of genetic ch...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lee GY,Yang WI,Jeung HC,Kim SC,Seo MY,Park CH,Chung HC,Rha SY

    更新日期:2007-09-03 00:00:00

  • Effect of sample stratification on dairy GWAS results.

    abstract:BACKGROUND:Artificial insemination and genetic selection are major factors contributing to population stratification in dairy cattle. In this study, we analyzed the effect of sample stratification and the effect of stratification correction on results of a dairy genome-wide association study (GWAS). Three methods for s...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ma L,Wiggans GR,Wang S,Sonstegard TS,Yang J,Crooker BA,Cole JB,Van Tassell CP,Lawlor TJ,Da Y

    更新日期:2012-10-06 00:00:00