Predicting gene expression levels from codon biases in α-proteobacterial genomes

被引：33

作者：

Karlin, S ^{[1
]}

Barnett, MJ

Campbell, AM

Fisher, RF

Mrázek, J

机构：

[1] Stanford Univ, Dept Math, Stanford, CA 94305 USA

[2] Stanford Univ, Dept Biol Sci, Stanford, CA 94305 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2003年 / 100卷 / 12期

关键词：

D O I：

10.1073/pnas.1232298100

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Predicted highly expressed (PHX) genes in five currently available high G+C complete alpha-proteobacterial genomes are analyzed. These include: the nitrogen-fixing plant symbionts Sinorhizobium meliloti (SINME) and Mesorhizobium loti (MESLO), the nonpathogenic aquatic bacterium Caulobacter crescentus (CAUCR), the plant pathogen Agrobacterium tumefaciens (AGRTU), and the mammalian pathogen Brucella melitensis (BRUME). Three of these genomes, SINME, AGRTU, and BRUME, contain multiple chromosomes or megaplasmids (>1 Mb length). PHX genes in these genomes are concentrated mainly in the major (largest) chromosome with few PHX genes found in the secondary chromosomes and megaplasmids. Tricarboxylic acid cycle and aerobic respiration genes are strongly PHX in all five genomes, whereas anaerobic pathways of glycolysis and fermentation are mostly not PHX. Only in MESLO (but not SINME) and BRUME are most glycolysis genes PHX Many flagellar genes are PHX in MESLO and CAUCR, but mostly are not PHX in SINME and AGRTU. The nonmotile BRUME also carries many flagellar genes but these are generally not PHX and all but one are located in the second chromosome. CAUCR stands out among available prokaryotic genomes with 25 PHX TonB-dependent receptors. These are putatively involved in uptake of iron ions and other nonsoluble compounds.

引用

页码：7313 / 7318

页数：6

共 23 条

[1] Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid [J].

Barnett, MJ ;

Fisher, RF ;

Jones, T ;

Komp, C ;

Abola, AP ;

Barloy-Hubler, F ;

Bowser, L ;

Capela, D ;

Galibert, F ;

Gouzy, J ;

Gurjal, M ;

Hong, A ;

Huizar, L ;

Hyman, RW ;

Kahn, D ;

Kahn, ML ;

Kalman, S ;

Keating, DH ;

Palm, C ;

Peck, MC ;

Surzycki, R ;

Wells, DH ;

Yeh, KC ;

Davis, RW ;

Federspiel, NA ;

Long, SR .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (17) :9883-9888

[2] Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA [J].

Campbell, A ;

Mrázek, J ;

Karlin, S .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (16) :9184-9189

[3] Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021 [J].

Capela, D ;

Barloy-Hubler, F ;

Gouzy, J ;

Bothe, G ;

Ampe, F ;

Batut, J ;

Boistard, P ;

Becker, A ;

Boutry, M ;

Cadieu, E ;

Dréano, S ;

Gloux, S ;

Godrie, T ;

Goffeau, A ;

Kahn, D ;

Kiss, E ;

Lelaure, V ;

Masuy, D ;

Pohl, T ;

Portetelle, D ;

Pühler, A ;

Purnelle, B ;

Ramsperger, U ;

Renard, C ;

Thébault, P ;

Vandenbol, M ;

Weidner, S ;

Galibert, F .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (17) :9877-9882

[4] The Escherichia coli RNA degradosome:: structure, function and relationship to other ribonucleolytic multienyzme complexes [J].

Carpousis, AJ .

BIOCHEMICAL SOCIETY TRANSACTIONS, 2002, 30 :150-155

[5] The genome sequence of the facultative intracellular pathogen Brucella melitensis [J].

DelVecchio, VG ;

Kapatral, V ;

Redkar, RJ ;

Patra, G ;

Mujer, C ;

Los, T ;

Ivanova, N ;

Anderson, I ;

Bhattacharyya, A ;

Lykidis, A ;

Reznik, G ;

Jablonski, L ;

Larsen, N ;

D'Souza, M ;

Bernal, A ;

Mazur, M ;

Goltsman, E ;

Selkov, E ;

Elzer, PH ;

Hagius, S ;

O'Callaghan, D ;

Letesson, JJ ;

Haselkorn, R ;

Kyrpides, N ;

Overbeek, R .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (01) :443-448

[6] The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti [J].

Finan, TM ;

Weidner, S ;

Wong, K ;

Buhrmester, J ;

Chain, P ;

Vorhölter, FJ ;

Hernandez-Lucas, I ;

Becker, A ;

Cowie, A ;

Gouzy, J ;

Golding, B ;

Pühler, A .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (17) :9889-9894

[7] The composite genome of the legume symbiont Sinorhizobium meliloti [J].

Galibert, F ;

Finan, TM ;

Long, SR ;

Pühler, A ;

Abola, P ;

Ampe, F ;

Barloy-Hubler, F ;

Barnett, MJ ;

Becker, A ;

Boistard, P ;

Bothe, G ;

Boutry, M ;

Bowser, L ;

Buhrmester, J ;

Cadieu, E ;

Capela, D ;

Chain, P ;

Cowie, A ;

Davis, RW ;

Dréano, S ;

Federspiel, NA ;

Fisher, RF ;

Gloux, S ;

Godrie, T ;

Goffeau, A ;

Golding, B ;

Gouzy, J ;

Gurjal, M ;

Hernandez-Lucas, I ;

Hong, A ;

Huizar, L ;

Hyman, RW ;

Jones, T ;

Kahn, D ;

Kahn, ML ;

Kalman, S ;

Keating, DH ;

Kiss, E ;

Komp, C ;

Lalaure, V ;

Masuy, D ;

Palm, C ;

Peck, MC ;

Pohl, TM ;

Portetelle, D ;

Purnelle, B ;

Ramsperger, U ;

Surzycki, R ;

Thébault, P ;

Vandenbol, M .

SCIENCE, 2001, 293 (5530) :668-672

[8] Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58 [J].

Goodner, B ;

Hinkle, G ;

Gattung, S ;

Miller, N ;

Blanchard, M ;

Qurollo, B ;

Goldman, BS ;

Cao, YW ;

Askenazi, M ;

Halling, C ;

Mullin, L ;

Houmiel, K ;

Gordon, J ;

Vaudin, M ;

Iartchouk, O ;

Epp, A ;

Liu, F ;

Wollam, C ;

Allinger, M ;

Doughty, D ;

Scott, C ;

Lappas, C ;

Markelz, B ;

Flanagan, C ;

Crowell, C ;

Gurson, J ;

Lomo, C ;

Sear, C ;

Strub, G ;

Cielo, C ;

Slater, S .

SCIENCE, 2001, 294 (5550) :2323-2328

[9]

Kaneko T, 2000, DNA RES, V7, P331, DOI 10.1093/dnares/7.6.331

[10] Predicted highly expressed genes of diverse prokaryotic genomes [J].

Karlin, S ;

Mrázek, J .

JOURNAL OF BACTERIOLOGY, 2000, 182 (18) :5238-5250

← 1 2 3 →