The iron-directed, coordinate regulation of genes depends on the fur (ferric uptake regulator) gene product, which acts as an iron-responsive, transcriptional repressor protein. To investigate the biological function of a fur homolog in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1, a fur knockout strain (FUR1) was generated by suicide plasmid integration into this gene and characterized using phenotype assays, DNA microarrays containing 691 arrayed genes, and two-dimensional polyacrylamide gel electrophoresis. Physiological studies indicated that FUR1 was similar to the wild-type strain when they were compared for anaerobic growth and reduction of various electron acceptors. Transcription profiling, however, revealed that genes with predicted functions in electron transport, energy metabolism, transcriptional regulation, and oxidative stress protection were either repressed (ccoNQ, etrA, cytochrome b and c maturation-encoding genes, qor, yiaY, sodB, rpoH, phoB, and chvI) or induced (yggW, pdhC, prpC, aceE, fdhD, and ppc) in the fur mutant. Disruption of fur also resulted in derepression of genes (hxuC, alcC, fhuA, hemR, irgA, and ompW) putatively involved in iron uptake. This agreed with the finding that the fur mutant produced threefold-higher levels of siderophore than the wild-type strain under conditions of sufficient iron. Analysis of a subset of the FUR1 proteome (i.e., primarily soluble cytoplasmic and periplasmic proteins) indicated that 11 major protein species reproducibly showed significant (P < 0.05) differences in abundance relative to the wild type. Protein identification using mass spectrometry indicated that the expression of two of these proteins (SodB and AlcC) correlated with the microarray data. These results suggest a possible regulatory role of S. oneidensis MR-1 Fur in energy metabolism that extends the traditional model of Fur as a negative regulator of iron acquisition systems.

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A comparative analysis of protein identification for a total of 162 protein spots separated by two-dimensional gel electrophoresis from two fully sequenced archaea, Methanococcus jannaschii and Pyrococcus furiosus, using MALDI-TOF peptide mass mapping (PMM) and LC-MS/MS is presented. 100% of the gel spots analyzed were successfully matched to the predicted proteins in the two corresponding open reading frame databases by LC-MS/MS while 97% of them were identified by MALDI-TOF PMM. The high success rate from the PMM resulted from sample desalting/concentrating with ZipTip C18 and optimization of several PMM search parameters including a 25 ppm average mass tolerance and the application of two different protein molecular weight search windows. By using this strategy, low-molecular weight (Ͻ23 kDa) proteins could be identified unambiguously with less than 5 peptide matches. Nine percent of spots were identified as containing multiple proteins. By using LC-MS/MS, 50% of the spots analyzed were identified as containing multiple proteins. LC-MS/MS demonstrated better protein sequence coverage than MALDI-TOF PMM over the entire mass range of proteins identified. MALDI-TOF and PMM produced unique peptide molecular weight matches that were not identified by LC-MS/MS. By incorporating amino acid sequence modifications into database searches, combined sequence coverage obtained from these two complimentary ionization methods exceeded 50% for ϳ70% of the 162 spots analyzed. This improved sequence coverage in combination with enzymatic digestions of different specificity is proposed as a method for analysis of post-translational modification from 2D-gel separated proteins. (J Am Soc Mass Spectrom 2003, 14, 957-970)

Shewanella oneidensis MR-1 is a mesophilic bacterium with a maximum growth temperature of Ϸ35°C but the ability to grow over a wide range of temperatures, including temperatures near zero. At room temperature (Ϸ22°C) MR-1 grows with a doubling time of about 40 min, but when moved from 22°C to 3°C, MR-1 cells display a very long lag phase of more than 100 h followed by very slow growth, with a doubling time of Ϸ67 h. In comparison to cells grown at 22°C, the cold-grown cells formed long, motile filaments, showed many spheroplast-like structures, produced an array of proteins not seen at higher temperature, and synthesized a different pattern of cellular lipids. Frequent pilus-like structures were observed during the transition from 3 to 22°C.Shewanella oneidensis MR-1 was first isolated from sediments of Lake Oneida in New York State (20). The cells are gram-negative straight rods capable of moving by means of a single polar flagellum. S. oneidensis MR-1 is a mesophilic, facultative anaerobe having a respiratory type of metabolism, with an optimal growth temperature of Ϸ30°C. Lake Oneida is a shallow freshwater system that freezes over completely during the winter (from early to mid-December to mid-or late January, with complete ice-out in March or April), with ice thickness reaching up to 70 cm (19). During May, water temperatures begin to rise, reaching a maximum of 25°C in midsummer (19).Because of their ability to metabolically reduce metals such as U(VI), Tc(VII), and Cr(VI), organisms such as Shewanella are considered candidates for bioremediation of subsurface metal-contaminated areas. However, subsurface temperatures are often low, and predictions of the utility of Shewanella in such environments require an understanding of the effects of low temperatures on their metabolism and general ecology. Recently, it was shown that S. oneidensis MR-1, while capable of growth at low temperature, exhibited a growth transition at about 10°C, and below these temperatures showed a differential increase in rRNA synthesis compared to DNA synthesis (4). Here we report on other properties of MR-1 grown at low temperature (3°C), including a dramatically different phenotype with changes in morphology, growth rate, ultrastructure, and protein and lipid composition. MATERIALS AND METHODSCells of Shewanella oneidensis strain MR-1 (ATCC 700550) were grown overnight aerobically in batch cultures at 22°C in 150-ml flasks containing 50 ml of Luria-Bertani (LB) broth Miller (Difco) at 130 rpm. For growth measurements, new cultures were started by transferring 1.0 ml of the original culture to a 250-ml Erlenmeyer flask containing 100 ml of LB and incubated at 130 rpm at two temperatures (3 and 22°C). All incubations were done in triplicate. Cells analyzed for proteins and phospholipid fatty acids were harvested by centrifugation and washed with sterile phosphate-buffered saline buffer, wet weight was determined, and the cells were frozen at Ϫ70°C until analysis.The turbidity of the cultures was measured at 600 nm. For measuring cell ...

It is crucial to examine the physiological processes of psychrophiles at temperatures below 4 degrees C, particularly to facilitate extrapolation of laboratory results to in situ activity. Using two dimensional electrophoresis, we examined patterns of protein abundance during growth at 16, 4, and -4 degrees C of the eurypsychrophile Psychrobacter cryohalolentis K5 and report the first identification of cold inducible proteins (CIPs) present during growth at subzero temperatures. Growth temperature substantially reprogrammed the proteome; the relative abundance of 303 of the 618 protein spots detected (approximately 31% of the proteins at each growth temperature) varied significantly with temperature. Five CIPs were detected specifically at -4 degrees C; their identities (AtpF, EF-Ts, TolC, Pcryo_1988, and FecA) suggested specific stress on energy production, protein synthesis, and transport during growth at subzero temperatures. The need for continual relief of low-temperature stress on these cellular processes was confirmed via identification of 22 additional CIPs whose abundance increased during growth at -4 degrees C (relative to higher temperatures). Our data suggested that iron may be limiting during growth at subzero temperatures and that a cold-adapted allele was employed at -4 degrees C for transport of iron. In summary, these data suggest that low-temperature stresses continue to intensify as growth temperatures decrease to -4 degrees C.