Fan G

References (12)

Title : Complete genome sequencing of Hortaea werneckii M-3 for identifying polyester polyurethane degrading enzymes - Ling_2024_Mar.Genomics_75_101111
Author(s) : Ling M , Zhang K , Hu J , Huang X , Fan G , Grossart HP , Luo Z
Ref : Mar Genomics , 75 :101111 , 2024
Abstract : Hortaea werneckii M-3, a black yeast isolated from the marine sediment of the West Pacific, can utilize polyester polyurethane (PU, Impranil DLN) as a sole carbon source. Here, we present the complete genome of Hortaea werneckii M-3 with the focus on PU degradation enzymes. The total genome size is 38,167,921 bp, consisting of 186 contigs with a N50 length of 651,266 bp and a GC content of 53.06%. Genome annotation analysis predicts a total of 13,462 coding genes, which include 99 tRNAs and 105 rRNAs. Some genes encoding PU degrading enzymes including cutinase and urease are identified in this genome. The genome analysis of Hortaea werneckii M-3 will be helpful for further understanding the degradation mechanism of polyester PU by marine yeasts.
ESTHER : Ling_2024_Mar.Genomics_75_101111
PubMedSearch : Ling_2024_Mar.Genomics_75_101111
PubMedID: 38735674

Title : Association between CES1 rs2244613 and the pharmacokinetics and safety of dabigatran: Meta-analysis and quantitative trait loci analysis - Li_2022_Front.Cardiovasc.Med_9_959916
Author(s) : Li H , Zhang Z , Weng H , Qiu Y , Zubiaur P , Zhang Y , Fan G , Yang P , Vuorinen AL , Zuo X , Zhai Z , Wang C
Ref : Front Cardiovasc Med , 9 :959916 , 2022
Abstract : OBJECTIVE: To date, the influence of the carboxylesterase 1 (CES1) rs2244613 genotype on the pharmacokinetics (PKs) and safety of dabigatran remains controversial. Hence, a systematic review was performed to study the association between CES1 rs2244613 genotype and the PKs and safety of dabigatran and CES1 relative expression. METHODS: In addition to the three English databases (Web of Science, PubMed, and Embase), two Chinese databases (CNKI and Wanfang) were thoroughly revised. The mean differences (MD) and corresponding 95% confidence intervals (CI) were applied to evaluate the differences in PKs between the CES1 rs2244613 genotype. Odds ratio (OR) was used to study the risk for bleeding events between the CES1 rs2244613 genotypes. Subsequent expression quantitative trait loci (eQTL) analyses were performed to evaluate genotype-specific expressions in human tissues. RESULTS: Ten studies (n = 2,777) were included. CES1 rs2244613 G allele carriers exhibited significantly lower dabigatran trough concentrations compared to T allele carriers (MD: -8.00 ng/mL; 95% CI: -15.08 to -0.92; p = 0.03). The risk for bleeding events was significantly lower in carriers of the G allele compared to T allele carriers (OR: 0.65; 95% CI: 0.44-0.96; p = 0.03). Subsequent eQTL analysis showed significant genome-wide expressions in two human tissues, whole blood (p = 5.1 x 10(-10)) and liver (p = 6.2 x 10(-43)). CONCLUSION: Our meta-analysis indicated a definite relation between the CES1 rs2244613 genotype and tolerability variations or pharmacokinetic fluctuations. The carriers of T allele showed higher dabigatran concentrations; therefore, they would benefit from a dose reduction. SYSTEMATIC REVIEW REGISTRATION: [https://inplasy.com/inplasy-2022-6-0027/], identifier [NPLASY202260027].
ESTHER : Li_2022_Front.Cardiovasc.Med_9_959916
PubMedSearch : Li_2022_Front.Cardiovasc.Med_9_959916
PubMedID: 35990949

Title : Biochemical characterization of a novel feruloyl esterase from Burkholderia pyrrocinia B1213 and its application for hydrolyzing wheat bran - Fu_2022_3.Biotech_12_24
Author(s) : Fu Z , Zhu Y , Teng C , Fan G , Li X
Ref : 3 Biotech , 12 :24 , 2022
Abstract : In this study, a novel feruloyl esterase (BpFae) from Burkholderia pyrrocinia B1213 was purified, biochemically characterized, and applied in releasing ferulic acid from wheat bran. The molecular mass of BpFae was approximately 60 kDa by SDS-PAGE, and the enzyme was a homomultimer in solution. BpFae displayed maximum activity at pH 4.5-5.0 and was stable at pH 3.0-7.0. The optimal temperature for BpFae was 50 degreesC. BpFae activity was not affected by most metal ions tested and was significantly increased by Tween-20 and Triton-100. Purified BpFae exhibited a preference for methyl ferulate (41.78 U mg(-1)) over methyl p-coumarate (38.51 U mg(-1)) and methyl caffeate (35.36 U mg(-1)) and had the lowest activity on methyl sinapate (1.79 U mg(-1)). Under the optimum conditions, the K (m) and V (max) for methyl ferulate were 0.53 mM and 86.74 U mg(-1), respectively. Residues Ser209, His492, and Glu245 in the catalytic pocket of BpFae could form hydrogen bonds with the substrate and were crucial for catalytic activity and substrate specificity. When G11 xylanase XynA and BpFae were used separately for hydrolyzing de-starched wheat bran (DSWB), the ferulic acid released was undetectable and 1.78%, respectively, whereas it was increased to 59.26% using the mixture of the two enzymes. Thus, BpFae is considered an attractive candidate for the production of ferulic acid from agricultural by-products. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-03066-2.
ESTHER : Fu_2022_3.Biotech_12_24
PubMedSearch : Fu_2022_3.Biotech_12_24
PubMedID: 35036272
Gene_locus related to this paper: 9burk-BpFae

Title : Optimization of fermentation conditions for the production of recombinant feruloyl esterase from Burkholderia pyrrocinia B1213 - Fan_2020_3.Biotech_10_216
Author(s) : Fan G , Zhu Y , Fu Z , Sun B , Teng C , Yang R , Li X
Ref : 3 Biotech , 10 :216 , 2020
Abstract : Statistical experimental designs were used to optimize conditions for recombinant Burkholderia pyrrocinia feruloyl esterase (BpFae) production in bacteria under lactose induction. After optimization by single factor design, Plackett-Burman design, steepest ascent design and the response surface method, the optimal conditions for BpFae production were: 6 g/L lactose, pH 5.5, pre-induced period 5 h, 23 degreesC, shaker rotational speed of 240 rpm, medium volume of 50 mL/250 mL, inoculum size 0.2% (v/v), and a post-induced period of 32 h in a Luria-Bertani culture. The produced BpFae activity was 7.43 U/mL, which is 2.92 times higher than that obtained under optimal conditions using IPTG as the inducer. BpFae activity was 4.82 U/mL in a 5 L fermenter under the abovementioned optimal conditions. BpFae produced a small amount of ethyl acetate but had no effect on the synthesis of other important esters in Baijiu. The results underpin further investigations into BpFae characterization and potential applications.
ESTHER : Fan_2020_3.Biotech_10_216
PubMedSearch : Fan_2020_3.Biotech_10_216
PubMedID: 32355590
Gene_locus related to this paper: 9burk-BpFae

Title : Screening, purification and characterization of lipase from Burkholderia pyrrocinia B1213 - Li_2018_3.Biotech_8_387
Author(s) : Li J , Shen W , Fan G , Li X
Ref : 3 Biotech , 8 :387 , 2018
Abstract : A lipase producing strain B1213 isolated from soil was identified as Burkholderia pyrrocinia based on 16S rRNA gene and recA sequeence analysis, making this the first report on the presence of a lipase from B. pyrrocinia. Under an aqueous two-phase purification strategy, which included (ATPE)-ion-exchange chromatography (IEC)-gel and filtration chromatography (GFC), the specific activity of the 35-kDa lipase was determined to be 875.7 U/mg protein. The optimum pH and temperature of this lipase was pH 8.0 and 50 degreesC, respectively. The lipase retained > 85% activity in isopropanol and acetone at 30 degreesC for 10 min but the activity was reduced to 10.6% in n-hexane. Mg(2+), Al(3+), Mn(2+), and Fe(3+) enhanced lipase activity at both 1 mM and 5 mM concentrations. p-NPP, a long-chain acyl group 4-NP ester, appeared to be a good substrate candidate.
ESTHER : Li_2018_3.Biotech_8_387
PubMedSearch : Li_2018_3.Biotech_8_387
PubMedID: 30175024

Title : Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution - Li_2015_Nat.Biotechnol_33_524
Author(s) : Li F , Fan G , Lu C , Xiao G , Zou C , Kohel RJ , Ma Z , Shang H , Ma X , Wu J , Liang X , Huang G , Percy RG , Liu K , Yang W , Chen W , Du X , Shi C , Yuan Y , Ye W , Liu X , Zhang X , Liu W , Wei H , Wei S , Zhu S , Zhang H , Sun F , Wang X , Liang J , Wang J , He Q , Huang L , Cui J , Song G , Wang K , Xu X , Yu JZ , Zhu Y , Yu S
Ref : Nat Biotechnol , 33 :524 , 2015
Abstract : Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6% approximately 96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.
ESTHER : Li_2015_Nat.Biotechnol_33_524
PubMedSearch : Li_2015_Nat.Biotechnol_33_524
PubMedID: 25893780
Gene_locus related to this paper: gosra-a0a0d2rxs2 , gosra-a0a0d2tng2 , gosra-a0a0d2twz7 , goshi-a0a1u8hr03 , gosra-a0a0d2vdc5 , goshi-a0a1u8ljh5 , gosra-a0a0d2vj24 , goshi-a0a1u8pxd3 , gosra-a0a0d2sr31 , goshi-a0a1u8knd1 , goshi-a0a1u8nhw9 , goshi-a0a1u8mt09 , goshi-a0a1u8kis4 , goshi-a0a1u8ibk3 , goshi-a0a1u8ieg2 , goshi-a0a1u8iki6 , goshi-a0a1u8jvp4 , goshi-a0a1u8jw35 , gosra-a0a0d2pzd7 , goshi-a0a1u8ied7

Title : Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes - You_2014_Nat.Commun_5_5594
Author(s) : You X , Bian C , Zan Q , Xu X , Liu X , Chen J , Wang J , Qiu Y , Li W , Zhang X , Sun Y , Chen S , Hong W , Li Y , Cheng S , Fan G , Shi C , Liang J , Tom Tang Y , Yang C , Ruan Z , Bai J , Peng C , Mu Q , Lu J , Fan M , Yang S , Huang Z , Jiang X , Fang X , Zhang G , Zhang Y , Polgar G , Yu H , Li J , Liu Z , Ravi V , Coon SL , Yang H , Venkatesh B , Shi Q
Ref : Nat Commun , 5 :5594 , 2014
Abstract : Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers' tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates.
ESTHER : You_2014_Nat.Commun_5_5594
PubMedSearch : You_2014_Nat.Commun_5_5594
PubMedID: 25463417
Gene_locus related to this paper: 9gobi-a0a3b4bh68 , 9gobi-a0a3b4bmj6 , 9gobi-a0a3b4alj9 , 9gobi-a0a3b4biy6 , 9gobi-a0a3b4ah01 , 9gobi-a0a3b3z8m7 , 9gobi-a0a3b4aaj5 , 9gobi-a0a3b4b6y7

Title : Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome - Chalhoub_2014_Science_345_950
Author(s) : Chalhoub B , Denoeud F , Liu S , Parkin IA , Tang H , Wang X , Chiquet J , Belcram H , Tong C , Samans B , Correa M , Da Silva C , Just J , Falentin C , Koh CS , Le Clainche I , Bernard M , Bento P , Noel B , Labadie K , Alberti A , Charles M , Arnaud D , Guo H , Daviaud C , Alamery S , Jabbari K , Zhao M , Edger PP , Chelaifa H , Tack D , Lassalle G , Mestiri I , Schnel N , Le Paslier MC , Fan G , Renault V , Bayer PE , Golicz AA , Manoli S , Lee TH , Thi VH , Chalabi S , Hu Q , Fan C , Tollenaere R , Lu Y , Battail C , Shen J , Sidebottom CH , Canaguier A , Chauveau A , Berard A , Deniot G , Guan M , Liu Z , Sun F , Lim YP , Lyons E , Town CD , Bancroft I , Meng J , Ma J , Pires JC , King GJ , Brunel D , Delourme R , Renard M , Aury JM , Adams KL , Batley J , Snowdon RJ , Tost J , Edwards D , Zhou Y , Hua W , Sharpe AG , Paterson AH , Guan C , Wincker P
Ref : Science , 345 :950 , 2014
Abstract : Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
ESTHER : Chalhoub_2014_Science_345_950
PubMedSearch : Chalhoub_2014_Science_345_950
PubMedID: 25146293
Gene_locus related to this paper: braol-Q8GTM3 , braol-Q8GTM4 , brana-a0a078j4a9 , brana-a0a078e1m0 , brana-a0a078cd75 , brana-a0a078evd3 , brana-a0a078j4f0 , brana-a0a078cta5 , brana-a0a078cus4 , brana-a0a078f8c2 , brana-a0a078jql1 , brana-a0a078dgj3 , brana-a0a078hw50 , brana-a0a078cuu0 , brana-a0a078iyl8 , brana-a0a078dfa9 , brana-a0a078ic91 , brana-a0a078cnf7 , brana-a0a078fh41 , brana-a0a078ca65 , brana-a0a078ctc8 , brana-a0a078h021 , brana-a0a078h0h8 , brana-a0a078jx23 , brana-a0a078ci96 , brana-a0a078cqd7 , brana-a0a078dh94 , brana-a0a078h612 , brana-a0a078ild2 , brana-a0a078j2t3 , braol-a0a0d3dpb2 , braol-a0a0d3dx76 , brana-a0a078jxa8 , brana-a0a078i2k3 , braol-a0a0d3ef55 , brarp-m4dcj8 , brana-a0a078fw53 , brana-a0a078itf3 , brana-a0a078jsn1 , brana-a0a078jrt9 , brana-a0a078i6d2 , brana-a0a078jku0 , brana-a0a078fss7 , brana-a0a078i1l0 , brana-a0a078i402

Title : Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing - Qi_2014_Nat.Commun_5_4340
Author(s) : Qi X , Li MW , Xie M , Liu X , Ni M , Shao G , Song C , Kay-Yuen Yim A , Tao Y , Wong FL , Isobe S , Wong CF , Wong KS , Xu C , Li C , Wang Y , Guan R , Sun F , Fan G , Xiao Z , Zhou F , Phang TH , Tong SW , Chan TF , Yiu SM , Tabata S , Wang J , Xu X , Lam HM
Ref : Nat Commun , 5 :4340 , 2014
Abstract : Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement.
ESTHER : Qi_2014_Nat.Commun_5_4340
PubMedSearch : Qi_2014_Nat.Commun_5_4340
PubMedID: 25004933
Gene_locus related to this paper: soybn-i1k636 , soybn-i1j4c6 , glyso-a0a0b2sjw6 , soybn-a0a0r0i9y7 , soybn-a0a0r0j241 , soybn-i1kfz9 , glyso-a0a0b2rre9 , soybn-i1jx17

Title : Diversity and plasticity of the intracellular plant pathogen and insect symbiont Candidatus Liberibacter asiaticus as revealed by hypervariable prophage genes with intragenic tandem repeats - Zhou_2011_Appl.Environ.Microbiol_77_6663
Author(s) : Zhou L , Powell CA , Hoffman MT , Li W , Fan G , Liu B , Lin H , Duan Y
Ref : Applied Environmental Microbiology , 77 :6663 , 2011
Abstract : "Candidatus Liberibacter asiaticus" is a psyllid-transmitted, phloem-limited alphaproteobacterium and the most prevalent species of "Ca. Liberibacter" associated with a devastating worldwide citrus disease known as huanglongbing (HLB). Two related and hypervariable genes (hyv(I) and hyv(II)) were identified in the prophage regions of the Psy62 "Ca. Liberibacter asiaticus" genome. Sequence analyses of the hyv(I) and hyv(II) genes in 35 "Ca. Liberibacter asiaticus" DNA isolates collected globally revealed that the hyv(I) gene contains up to 12 nearly identical tandem repeats (NITRs, 132 bp) and 4 partial repeats, while hyv(II) contains up to 2 NITRs and 4 partial repeats and shares homology with hyv(I). Frequent deletions or insertions of these repeats within the hyv(I) and hyv(II) genes were observed, none of which disrupted the open reading frames. Sequence conservation within the individual repeats but an extensive variation in repeat numbers, rearrangement, and the sequences flanking the repeat region indicate the diversity and plasticity of "Ca. Liberibacter asiaticus" bacterial populations in the world. These differences were found not only in samples of distinct geographical origins but also in samples from a single origin and even from a single "Ca. Liberibacter asiaticus"-infected sample. This is the first evidence of different "Ca. Liberibacter asiaticus" populations coexisting in a single HLB-affected sample. The Florida "Ca. Liberibacter asiaticus" isolates contain both hyv(I) and hyv(II), while all other global "Ca. Liberibacter asiaticus" isolates contain either one or the other. Interclade assignments of the putative Hyv(I) and Hyv(II) proteins from Florida isolates with other global isolates in phylogenetic trees imply multiple "Ca. Liberibacter asiaticus" populations in the world and a multisource introduction of the "Ca. Liberibacter asiaticus" bacterium into Florida.
ESTHER : Zhou_2011_Appl.Environ.Microbiol_77_6663
PubMedSearch : Zhou_2011_Appl.Environ.Microbiol_77_6663
PubMedID: 21784907
Gene_locus related to this paper: libap-c6xgr3

Title : Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers - Varshney_2011_Nat.Biotechnol_30_83
Author(s) : Varshney RK , Chen W , Li Y , Bharti AK , Saxena RK , Schlueter JA , Donoghue MT , Azam S , Fan G , Whaley AM , Farmer AD , Sheridan J , Iwata A , Tuteja R , Penmetsa RV , Wu W , Upadhyaya HD , Yang SP , Shah T , Saxena KB , Michael T , McCombie WR , Yang B , Zhang G , Yang H , Wang J , Spillane C , Cook DR , May GD , Xu X , Jackson SA
Ref : Nat Biotechnol , 30 :83 , 2011
Abstract : Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.
ESTHER : Varshney_2011_Nat.Biotechnol_30_83
PubMedSearch : Varshney_2011_Nat.Biotechnol_30_83
PubMedID: 22057054
Gene_locus related to this paper: cajca-a0a151r9d2 , cajca-a0a151u2m0 , cajca-a0a151tes0 , cajca-a0a151u784 , cajca-a0a151sf79 , cajca-a0a151qu18 , cajca-a0a151sz37 , cajca-a0a151ss18 , cajca-a0a151rb44 , cajca-a0a151ryr0 , cajca-a0a151qzm6 , cajca-a0a151rsm6 , cajca-a0a151rsn1 , cajca-a0a151tig2 , cajca-a0a151rwt3 , cajca-a0a151rx08 , cajca-a0a151rws4 , cajca-a0a151r0b7

Title : Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae - McLeod_2004_J.Bacteriol_186_5842
Author(s) : McLeod MP , Qin X , Karpathy SE , Gioia J , Highlander SK , Fox GE , McNeill TZ , Jiang H , Muzny D , Jacob LS , Hawes AC , Sodergren E , Gill R , Hume J , Morgan M , Fan G , Amin AG , Gibbs RA , Hong C , Yu XJ , Walker DH , Weinstock GM
Ref : Journal of Bacteriology , 186 :5842 , 2004
Abstract : Rickettsia typhi, the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate hosts. Here we present the complete genome sequence of R. typhi (1,111,496 bp) and compare it to the two published rickettsial genome sequences: R. prowazekii and R. conorii. We identified 877 genes in R. typhi encoding 3 rRNAs, 33 tRNAs, 3 noncoding RNAs, and 838 proteins, 3 of which are frameshifts. In addition, we discovered more than 40 pseudogenes, including the entire cytochrome c oxidase system. The three rickettsial genomes share 775 genes: 23 are found only in R. prowazekii and R. typhi, 15 are found only in R. conorii and R. typhi, and 24 are unique to R. typhi. Although most of the genes are colinear, there is a 35-kb inversion in gene order, which is close to the replication terminus, in R. typhi, compared to R. prowazekii and R. conorii. In addition, we found a 124-kb R. typhi-specific inversion, starting 19 kb from the origin of replication, compared to R. prowazekii and R. conorii. Inversions in this region are also seen in the unpublished genome sequences of R. sibirica and R. rickettsii, indicating that this region is a hot spot for rearrangements. Genome comparisons also revealed a 12-kb insertion in the R. prowazekii genome, relative to R. typhi and R. conorii, which appears to have occurred after the typhus (R. prowazekii and R. typhi) and spotted fever (R. conorii) groups diverged. The three-way comparison allowed further in silico analysis of the SpoT split genes, leading us to propose that the stringent response system is still functional in these rickettsiae.
ESTHER : McLeod_2004_J.Bacteriol_186_5842
PubMedSearch : McLeod_2004_J.Bacteriol_186_5842
PubMedID: 15317790
Gene_locus related to this paper: ricco-PTRB , ricty-q68vs9 , ricty-q68w06 , ricty-q68w12 , ricty-q68w56 , ricty-q68wq9 , ricty-q68wt4 , ricty-q68x29 , ricty-q68xj3