The amino-terminal region of the long-chain fatty acid transport protein FadL contains an externally exposed domain required for bacteriophage T2 binding

Integrated biochemical, transcriptomic and metabolomic analyses provide insight into heat stress response in Yangtze sturgeon (Acipenser dabryanus)

Temperature fluctuations caused by climate change and global warming pose a great threat to various species. Most fish are particularly vulnerable to elevated temperatures. Understanding the mechanism of high-temperature tolerance in fish can be beneficial for proposing effective strategies to help fish cope with global warming. In this study, we systematically studied the effects of high temperature on Acipenser dabryanus, an ancient living fossil and flagship species of the Yangtze River, at the histological, biochemical, transcriptomic and metabolomic levels. Intestinal and liver tissues from the control groups (18 °C) and acute heat stress groups (30 °C) of A. dabryanus were sampled for histological observation and liver tissues were assessed for transcriptomic and metabolomic profiling. Histopathological analysis showed that the intestine and liver tissues were damaged after heat stress. The plasma cortisol content and the levels of oxidative stress markers (catalase/glutathione reductase) and two aminotransferases (aspartate aminotransferase/alanine aminotransferase) increased significantly in response to acute heat stress. Transcriptomic and metabolomic methods showed 6707 upregulated and 4189 downregulated genes and 64 upregulated and 78 downregulated metabolites in the heat stress group. Heat shock protein (HSP) genes showed striking changes in expression under heat stress, with 21 genes belonging to the HSP30, HSP40, HSP60, HSP70 and HSP90 families significantly upregulated by short-term heat stress. The majority of genes associated with ubiquitin and various immune-related pathways were also markedly upregulated in the heat stress group. In addition, the combined analysis of metabolites and gene profiles suggested an enhancement of amino acid metabolism and glycometabolism and the suppression of fatty acid metabolism during heat stress, which could be a potential energy conservation strategy for A. dabryanus. To the best of our knowledge, the present study represents the first attempt to reveal the mechanisms of heat stress responses in A. dabryanus, which can provide insights into improved cultivation of fish in response to global warming.

Hydrophobic cell surface display system of PETase as a sustainable biocatalyst for PET degradation

Remarkably, a hydrolase from Ideonella sakaiensis 201-F6, termed PETase, exhibits great potential in polyethylene terephthalate (PET) waste management due to it can efficiently degrade PET under moderate conditions. However, its low yield and poor accessibility to bulky substrates hamper its further industrial application. Herein a multigene fusion strategy is introduced for constructing a hydrophobic cell surface display (HCSD) system in Escherichia coli as a robust, recyclable, and sustainable whole-cell catalyst. The truncated outer membrane hybrid protein FadL exposed the PETase and hydrophobic protein HFBII on the surface of E. coli with efficient PET accessibility and degradation performance. E. coli containing the HCSD system changed the surface tension of the bacterial solution, resulting in a smaller contact angle (83.9 ± 2° vs. 58.5 ± 1°) of the system on the PET surface, thus giving a better opportunity for PETase to interact with PET. Furthermore, pretreatment of PET with HCSD showed rougher surfaces with greater hydrophilicity (water contact angle of 68.4 ± 1° vs. 106.1 ± 2°) than the non-pretreated ones. Moreover, the HCSD system showed excellent sustainable degradation performance for PET bottles with a higher degradation rate than free PETase. The HCSD degradation system also had excellent stability, maintaining 73% of its initial activity after 7 days of incubation at 40°C and retaining 70% activity after seven cycles. This study indicates that the HCSD system could be used as a novel catalyst for efficiently accelerating PET biodegradation.

Comprehensive transcriptome analysis reveals the effect of feeding rhythm on the immunity and metabolism of Acipenser dabryanus

Acipenser dabryanus is a species endemic to Yangtze River drainage in China and is listed as a critical endangered species on the IUCN Red List. In the present study, the liver and spleen transcriptomes were analyzed by comparing the data of A. dabryanus that experienced nine different feeding rhythms (once a day diurnal, T1; two times a day diurnal, T2; three times a day diurnal, T3; four times a day, T4; five times a day, T5; six times a day, T6; once a day nocturnal, Tn1; two times a day nocturnal, Tn2; and three times a day nocturnal, Tn3). Transcriptome sequencing generated 1,901,236,482 clean reads, encompassing 570.4 Gb of sequence data. The reads were assembled into 287,372 unigenes with an average length of 803 bp and an N50 of 1004 bp. KEGG analysis showed that 1,080, 1,030, and 1216 unigenes were annotated to lipid metabolism, amino acid metabolism and carbohydrate metabolism, respectively, and 2549 unigenes were annotated to the immune system category. Differentially expressed genes (DEGs) between different feeding frequency groups or between nighttime and daytime feeding were obtained and functionally enriched. Importantly, DEGs participating in nutrition metabolism and various immunoregulation pathways and their expression profiles in A. dabryanus were discussed. Interestingly, the majority of key genes related to lipid metabolism or in immunodependent gene families, such as antimicrobial peptides, Toll-like receptors, chemokines, NOD-like receptors, B cell receptors and the major histocompatibility complex, were all significantly upregulated in animals in the T6 group compared to the characteristics of animals in the T2 group that had a normal feeding frequency. In addition, light/dark rhythm also affected the immunity of A. dabryanus, and fish fed at night possessed an improved immune response than fish fed at daytime. Our study suggested that feeding six times a day is optimal for A. dabryanus juvenile growth as it enhances the organism's nutrition metabolism and immune function.

Screening of Polyvalent Phage-Resistant Escherichia coli Strains Based on Phage Receptor Analysis

Bacteria-based biotechnology processes are constantly under threat from bacteriophage infection, with phage contamination being a non-neglectable problem for microbial fermentation. The essence of this problem is the complex co-evolutionary relationship between phages and bacteria. The development of phage control strategies requires further knowledge about phage-host interactions, while the widespread use of Escherichia coli strain BL21 (DE3) in biotechnological processes makes the study of phage receptors in this strain particularly important. Here, eight phages infecting E. coli BL21 (DE3) via different receptors were isolated and subsequently identified as members of the genera T4virus, Js98virus, Felix01virus, T1virus, and Rtpvirus. Phage receptors were identified by whole-genome sequencing of phage-resistant E. coli strains and sequence comparison with wild-type BL21 (DE3). Results showed that the receptors for the isolated phages, designated vB_EcoS_IME18, vB_EcoS_IME253, vB_EcoM_IME281, vB_EcoM_IME338, vB_EcoM_IME339, vB_EcoM_IME340, vB_EcoM_IME341, and vB_EcoS_IME347 were FhuA, FepA, OmpF, lipopolysaccharide, Tsx, OmpA, FadL, and YncD, respectively. A polyvalent phage-resistant BL21 (DE3)-derived strain, designated PR8, was then identified by screening with a phage cocktail consisting of the eight phages. Strain PR8 is resistant to 23 of 32 tested phages including Myoviridae and Siphoviridae phages. Strains BL21 (DE3) and PR8 showed similar expression levels of enhanced green fluorescent protein. Thus, PR8 may be used as a phage resistant strain for fermentation processes. The findings of this study contribute significantly to our knowledge of phage-host interactions and may help prevent phage contamination in fermentation.

Molecular analysis of porin gene transcription in heterogenotypic multidrug-resistant Escherichia coli isolates from scouring calves

BACKGROUND

Despite evidence that altered membrane porins may impair microbial drug uptake thereby potentially compounding efflux pump-mediated multidrug resistance, few studies have evaluated gene transcription to identify multidrug-resistance-associated porins and other potential drug targets.

METHODS

Genes that encode six membrane porins (fadL, lamB, ompC, ompF, ompW and yiaT) and two membrane proteins (tolC and ompT) were assessed by PCR and by quantitative real-time PCR (qRT-PCR) analysis of 10 multidrug-resistant (MDR) and 10 antibiotic-susceptible (AS) Escherichia coli isolates. The mean DeltaDeltaCt values for the study E. coli genes were analysed by the Wilcoxon test (P = 0.05).

RESULTS

All 20 E. coli isolates tested positive for tolC, lamB, ompC, ompF genes, while 10 MDR and 9/10 (90%) AS isolates were positive for the fadL gene. Seven out of 10 (70%) MDR and 7/10 (70%) AS isolates were positive for the yiaT gene, while 7/10 (70%) MDR and only 4/10 (40%) AS isolates were positive for the ompT gene. The mean DeltaDeltaCt values for the tolC and yiaT genes were significantly higher in MDR than in AS isolates (Wilcoxon test; P < 0.05). No significant difference was seen with respect to fadL, lamB, ompC, ompF, ompT and ompW gene transcription (Wilcoxon test; P > 0.05).

CONCLUSIONS

Findings suggest up-regulated transcription of tolC and yiaT genes in the MDR E. coli isolates. These results indirectly suggest that TolC and YiaT proteins may play some role(s) in multidrug resistance, but proteomic studies are needed before the two proteins are considered potential drug targets.

Dynamic mechanism of fatty acid transport across cellular membranes through FadL: molecular dynamics simulations

FadL is an important member of the family of fatty acid transport proteins within membranes. In this study, 11 conventional molecular dynamics (CMD) and 25 steered molecular dynamics (SMD) simulations were performed to investigate the dynamic mechanism of transport of long-chain fatty acids (LCFAs) across FadL. The CMD simulations addressed the intrinsically dynamic behavior of FadL. Both the CMD and SMD simulations revealed that a fatty acid molecule can move diffusively to a high-affinity site (HAS) from a low-affinity site (LAS). During this process, the swing motion of the L3 segment and the hydrophobic interaction between the fatty acid and FadL could play important roles. Furthermore, 22 of the SMD simulations revealed that fatty acids can pass through the gap between the hatch domain and the transmembrane domain (TMD) by different pathways. SMD simulations identified nine possible pathways for dodecanoic acid (DA) threading the barrel of FadL. The binding free energy profiles between DA and FadL along the MD trajectories indicate that all of the possible pathways are energetically favorable for the transport of fatty acids; however, one pathway (path VI) might be the most probable pathway for DA transport. The reasonability and reliability of this study were further demonstrated by correlating the MD simulation results with the available mutagenesis results. On the basis of the simulations, a mechanism for the full-length transport process of DA from the extracellular side to the periplasmic space mediated by FadL is proposed.

Display of bacterial lipase on the Escherichia coli cell surface by using FadL as an anchoring motif and use of the enzyme in enantioselective biocatalysis

We have developed a novel cell surface display system by employing FadL as an anchoring motif, which is an outer membrane protein involved in long-chain fatty acid transport in Escherichia coli. A thermostable Bacillus sp. strain TG43 lipase (44.5 kDa) could be successfully displayed on the cell surface of E. coli in an active form by C-terminal deletion-fusion of lipase at the ninth external loop of FadL. The localization of the truncated FadL-lipase fusion protein on the cell surface was confirmed by confocal microscopy and Western blot analysis. Lipase activity was mainly detected with whole cells, but not with the culture supernatant, suggesting that cell lysis was not a problem. The activity of cell surface-displayed lipase was examined at different temperatures and pHs and was found to be the highest at 50 degrees C and pH 9 to 10. Cell surface-displayed lipase was quite stable, even at 60 and 70 degrees C, and retained over 90% of the full activity after incubation at 50 degrees C for a week. As a potential application, cell surface-displayed lipase was used as a whole-cell catalyst for kinetic resolution of racemic methyl mandelate. In 36 h of reaction, (S)-mandelic acid could be produced with the enantiomeric excess of 99% and the enantiomeric ratio of 292, which are remarkably higher than values obtained with crude lipase or cross-linked lipase crystal. These results suggest that FadL may be a useful anchoring motif for displaying enzymes on the cell surface of E. coli for whole-cell biocatalysis.

Molecular basis of bacterial outer membrane permeability revisited

Gram-negative bacteria characteristically are surrounded by an additional membrane layer, the outer membrane. Although outer membrane components often play important roles in the interaction of symbiotic or pathogenic bacteria with their host organisms, the major role of this membrane must usually be to serve as a permeability barrier to prevent the entry of noxious compounds and at the same time to allow the influx of nutrient molecules. This review summarizes the development in the field since our previous review (H. Nikaido and M. Vaara, Microbiol. Rev. 49:1-32, 1985) was published. With the discovery of protein channels, structural knowledge enables us to understand in molecular detail how porins, specific channels, TonB-linked receptors, and other proteins function. We are now beginning to see how the export of large proteins occurs across the outer membrane. With our knowledge of the lipopolysaccharide-phospholipid asymmetric bilayer of the outer membrane, we are finally beginning to understand how this bilayer can retard the entry of lipophilic compounds, owing to our increasing knowledge about the chemistry of lipopolysaccharide from diverse organisms and the way in which lipopolysaccharide structure is modified by environmental conditions.

Transmembrane movement of exogenous long-chain fatty acids: proteins, enzymes, and vectorial esterification

The processes that govern the regulated transport of long-chain fatty acids across the plasma membrane are quite distinct compared to counterparts involved in the transport of hydrophilic solutes such as sugars and amino acids. These differences stem from the unique physical and chemical properties of long-chain fatty acids. To date, several distinct classes of proteins have been shown to participate in the transport of exogenous long-chain fatty acids across the membrane. More recent work is consistent with the hypothesis that in addition to the role played by proteins in this process, there is a diffusional component which must also be considered. Central to the development of this hypothesis are the appropriate experimental systems, which can be manipulated using the tools of molecular genetics. Escherichia coli and Saccharomyces cerevisiae are ideally suited as model systems to study this process in that both (i) exhibit saturable long-chain fatty acid transport at low ligand concentrations, (ii) have specific membrane-bound and membrane-associated proteins that are components of the transport apparatus, and (iii) can be easily manipulated using the tools of molecular genetics. In both systems, central players in the process of fatty acid transport are fatty acid transport proteins (FadL or Fat1p) and fatty acyl coenzyme A (CoA) synthetase (FACS; fatty acid CoA ligase [AMP forming] [EC 6.2.1.3]). FACS appears to function in concert with FadL (bacteria) or Fat1p (yeast) in the conversion of the free fatty acid to CoA thioesters concomitant with transport, thereby rendering this process unidirectional. This process of trapping transported fatty acids represents one fundamental mechanism operational in the transport of exogenous fatty acids.

Biochemical evidence against protein-mediated uptake of myristic acid in the bioluminescent marine bacterium Vibrio harveyi

The bioluminescent marine bacterium, Vibrio harveyi, can utilize exogenous myristic acid (14:0) for beta-oxidation, phospholipid and lipid A synthesis, and as an source of myristyl aldehyde for light emission in the V. harveyi dark mutant M17. A variety of genetic and biochemical strategies were employed in an attempt to isolate V. harveyi mutants defective in myristate uptake and to characterize proteins involved in this process. Although [3H]myristate uptake in a tritium suicide experiment decreased the survival of nitrosoguanidine-treated M17 cells by a factor of 10(5), none of the surviving cells characterized were defective in either incorporation of exogenous myristate into phospholipid or stimulation of light emission. These parameters were also unaffected when intact M17 cells were treated with proteases. Moreover, M17 double mutants selected on the basis of diminished luminescence response to myristate all incorporated [3H]myristate into lipids normally. Finally, no resistant colonies were obtained using the bacteriocidal fatty acid analogue, 11-bromoundecanoate, and experiments with decanoate (10:0) indicated that the V. harveyi cell envelope is very sensitive to physical disruption by fatty acids. Taken together, these results support an unfacilitated uptake of myristic acid in V. harveyi, in contrast with the regulated vectorial transport and activation of long chain fatty acids in Escherichia coli.

Murine FATP alleviates growth and biochemical deficiencies of yeast fat1Delta strains

Saccharomyces cerevisiae is an ideal model eukaryote for studying fatty-acid transport. Yeast are auxotrophic for unsaturated fatty acids when grown under hypoxic conditions or when the fatty-acid synthase inhibitor cerulenin is included in the growth media. The FAT1 gene encodes a protein, Fat1p, which is required for maximal levels of fatty-acid import and has an acyl CoA synthetase activity specific for very-long-chain fatty acids suggesting this protein plays a pivotal role in fatty-acid trafficking. In the present work, we present evidence that Fat1p and the murine fatty-acid transport protein (FATP) are functional homologues. FAT1 is essential for growth under hypoxic conditions and when cerulenin was included in the culture media in the presence or absence of unsaturated fatty acids. FAT1 disruptants (fat1Delta) fail to accumulate the fluorescent long-chain fatty acid fatty-acid analogue 4, 4-difluoro-5-methyl-4-bora-3a,4a-diaza-s-indacene-3-do decanoic acid (C1-BODIPY-C12), have a greatly diminished capacity to transport exogenous long-chain fatty acids, and have very long-chain acyl CoA synthetase activities that were 40% wild-type. The depression in very long-chain acyl CoA synthetase activities were not apparent in cells grown in the presence of oleate. Additionally, beta-oxidation of exogenous long-chain fatty acids is depressed to 30% wild-type levels. The reduction of beta-oxidation was correlated with a depression of intracellular oleoyl CoA levels in the fat1Delta strain following incubation of the cells with exogenous oleate. Expression of either Fat1p or murine FATP from a plasmid in a fat1Delta strain restored these phenotypic and biochemical deficiencies. Fat1p and FATP restored growth of fat1Delta cells in the presence of cerulenin and under hypoxic conditions. Furthermore, fatty-acid transport was restored and was found to be chain length specific: octanoate, a medium-chain fatty acid was transported in a Fat1p- and FATP-independent manner while the long-chain fatty acids myristate, palmitate, and oleate required either Fat1p or FATP for maximal levels of transport. Lignoceryl CoA synthetase activities were restored to wild-type levels in fat1Delta strains expressing either Fat1p or FATP. Fat1p or FATP also restored wild-type levels of beta-oxidation of exogenous long-chain fatty acids. These data show that Fat1p and FATP are functionally equivalent when expressed in yeast and play a central role in fatty-acid trafficking.