High-throughput comparison of gene fitness among related bacteria

ABSTRACT: BACKGROUND: The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains to reveal differences not apparent at the gene sequence level. RESULTS: A transposon Tn5 derivative was used to construct mutants in Salmonella Typhimurium ATCC14028 (STM1) and Salmonella Typhi Ty2 (STY1), which were then grown in rich media. The locations of 234,152 and 53,556 integration sites, respectively, were mapped by sequencing. These data were compared to similar data available for a different Ty2 strain (STY2) and essential genes identified in E. coli K-12 (ECO). Of 277 genes considered essential in ECO, all had syntenic homologs in STM1, STY1, and STY2, and all but nine genes were either devoid of Tn insertions or had very few. For three of these nine genes, part of the annotated gene lacked Tn integrations (yejM, ftsN and murB). At least one of the other six genes, trpS, had a potentially functionally redundant gene encoded elsewhere in Salmonella but not in ECO. An additional 165 genes were almost entirely devoid of transposon integrations in all three Salmonella strains examined, including many genes associated with protein and DNA synthesis. Four of these genes (STM14_1498.L, STM14_2872, STM14_3360.RJ, and STM14_5442) are not found in E. coli. Notable differences in the extent of gene selection were also observed among the three different Salmonella isolates. Mutations in hns, for example, were selected against in STM1 but not in the two STY strains, which have a defect in rpoS rendering hns nonessential. CONCLUSIONS: Comparisons among transposon integration profiles from different members of a species and among related species, all grown in similar conditions, identify differences in gene fitness among syntenic homologous genes. Further differences in fitness profiles among shared genes can be expected in other selective environments, with potential relevance for comparative systems biology.     

Nitrite oxidation in the Namibian oxygen minimum zone

Nitrite oxidation is the second step of nitrification. It is the primary source of oceanic nitrate, the predominant form of bioavailable nitrogen in the ocean. Despite its obvious importance, nitrite oxidation has rarely been investigated in marine settings. We determined nitrite oxidation rates directly in ¹⁵N-incubation experiments and compared the rates with those of nitrate reduction to nitrite, ammonia oxidation, anammox, denitrification, as well as dissimilatory nitrate/nitrite reduction to ammonium in the Namibian oxygen minimum zone (OMZ). Nitrite oxidation (⩽372 nM NO₂⁻ d⁻¹) was detected throughout the OMZ even when in situ oxygen concentrations were low to non-detectable. Nitrite oxidation rates often exceeded ammonia oxidation rates, whereas nitrate reduction served as an alternative and significant source of nitrite. Nitrite oxidation and anammox co-occurred in these oxygen-deficient waters, suggesting that nitrite-oxidizing bacteria (NOB) likely compete with anammox bacteria for nitrite when substrate availability became low. Among all of the known NOB genera targeted via catalyzed reporter deposition fluorescence in situ hybridization, only Nitrospina and Nitrococcus were detectable in the Namibian OMZ samples investigated. These NOB were abundant throughout the OMZ and contributed up to ∼9% of total microbial community. Our combined results reveal that a considerable fraction of the recently recycled nitrogen or reduced NO₃⁻ was re-oxidized back to NO₃⁻ via nitrite oxidation, instead of being lost from the system through the anammox or denitrification pathways.     

Species identity of geographically distinct populations of the glassy-winged sharpshooter parasitoid Gonatocerus ashmeadi: morphology, DNA sequences, and reproductive compatibility

Gonatocerus ashmeadi is a common and seemingly widespread egg parasitoid of Homalodisca coagulata, the glassy-winged sharpshooter (GWSS). Location records for G. ashmeadi indicate its natural range to be the southeastern USA and northeastern Mexico (which coincides with the presumed native range of GWSS), and possibly southern and central California (CA) (the adventive range of GWSS). The purpose of our work was to determine whether G. ashmeadi in the USA and northeastern Mexico is one species or a complex of reproductively incompatible sibling species. We used three approaches to determine the species identity of different G. ashmeadi populations: (1) reassessment of key morphological features using scanning electron microscopy (SEM) to determine if subtle morphological differences exist between G. ashmeadi populations which could indicate species differences; (2) to determine if molecular differences exist between G. ashmeadi populations collected from different regions by comparing mitochondrial and ribosomal DNA sequences; (3) mating compatibility studies to determine if different populations of G. ashmeadi are reproductively isolated, or if mating occurs, whether offspring are viable thereby defining species groups on the basis of successful interbreeding. Results from these three areas (morphology, DNA sequences, and reproductive compatibility) have been evaluated collectively; leading us to the conclusion that G. ashmeadi as it is currently viewed is a valid species and not an aggregate of morphologically indistinguishable cryptic species.     

Host plan preferences of Oscinella spp. (Diptera: Chloropidae) in the laboratory

The oviposition preferences of Oscinella frit, O. vastator, O. nitidissima, O. albiseta andO. nigerrima for differenct Gramineae were investigated in the laboratory. O. frit, laid most eggs on oats, Lolium multiflorum and Festuca rubra, relatively few eggs were laid on barley and virtually none on Dactylis glomerata None of the other Osinella species oviposted on cereals. Of the other species, O. vastator appeared to be the most polyphagous and the preferred hosts were L. multiflorum, Lolium perenne and Festuca pratensis; few eggs were laid on either F. rubra, Agrostis tenuis or Poa pratensis. The host ranges of the remaining species were much more limited. Although a few eggs were laid by O. nitidissima on Lolium, the preferred host was A. tenuis. Oscinella albiseta oviposited only on D. glomerata whilst nearly all the eggs laid by O. nigerrima were deposited on shoots of Arrhenatherum elatius. The distribution of eggs by O. frit on L. multiflorum and A. tenuis was different from that on oats; on grasses most eggs were laid inside withered leaf sheaths whereas on oats most were deposited inside the coleoptile. The oviposition sites of O. nitidissima, O. nigerrima and O. albiseta on their respective host grasses were similar to those of O. frit on grasses. O. frit laid most eggs on grasses which were at the five-leaf stage and tailoring.     

Deletions in the carboxyl-terminal region of Streptococcus gordonii glucosyltransferase affect cell-associated enzyme activity and sucrose-associated accumulation of growing cells.

The single glucosyltransferase (GTF) of Streptococcus gordonii Challis CH1 makes alpha 1,3- and alpha 1,6-linked glucans from sucrose. The GTF carboxyl-terminal region has six direct repeats thought to be involved in glucan binding. Strains with defined mutations in this region have been described recently (M. M. Vickerman, M. C. Sulavik, P. E. Minick, and D. B. Clewell, Infect. Immun. 64:5117-5128, 1996). Strain CH107 GTF has three internal direct repeats deleted; the 59 carboxyl-terminal amino acids are identical to those of the parental strain. This deletion resulted in decreased enzyme activity but did not affect the amount of cell-associated GTF protein. The GTFs of strains CH2RPE and CH4RPE have six and eight direct repeats, respectively, but are both missing the 14 carboxyl-terminal amino acids. Strain CH2RPE had significantly decreased levels of cell-associated GTF; this decrease was not obviated by the increased number of direct repeats in strain CH4RPE. Thus, the carboxyl-terminal amino acids appeared to influence the amount of cell-associated GTF more than the direct repeats. The qualitative and quantitative differences in the GTFs did not affect the abilities of these strains to accumulate on hydroxyapatite beads in the absence of sucrose. However, when sucrose was added as a substrate for GTF, the mutant strains were unable to accumulate on these surfaces to the same extent as the parent. These differences in sucrose-associated accumulation may be due to changes in the nature of the glucans produced by the different enzymes and/or cohesive interactions between these glucans and the GTF on the surfaces of the growing streptococci.     

Arabidopsis At5g39790 encodes a chloroplast-localized,carbohydrate-binding,coiled-coil domain-containing putative scaffold protein

Background  

Starch accumulation and degradation in chloroplasts is accomplished by a suite of over 30 enzymes. Recent work has emphasized the importance of multi-protein complexes amongst the metabolic enzymes, and the action of associated non-enzymatic regulatory proteins. Arabidopsis At5g39790 encodes a protein of unknown function whose sequence was previously demonstrated to contain a putative carbohydrate-binding domain.